It appears that it is possible though somewhat difficult to apply batch estimations generated by sva to the model given to DESeq/EdgeR/limma. In the case of limma it is fairly simple, but in the other two it is a bit more difficult. There is a nice discussion of this at: https://www.biostars.org/p/156186/ I am attempting to apply that logic to this data with limited success.
keepers <- list(
"wt_stex" = c("wt_st", "wt_ex"),
"mt_stex" = c("mt_st", "mt_ex"),
"st_wtmt" = c("mt_st", "wt_st"),
"ex_wtmt" = c("mt_ex", "wt_ex"))
pa_de <- all_pairwise(input=pa_expt,
parallel=FALSE,
model_batch=FALSE,
limma_method="robust")## Assuming no batch in model for testing pca.## Starting basic pairwise comparison.## Basic step 0/3: Filtering data.## Basic step 0/3: Normalizing data.## Basic step 0/3: Converting data.## Basic step 0/3: Transforming data.## Basic step 1/3: Creating median and variance tables.## Basic step 2/3: Performing 21 comparisons.## Basic step 3/3: Creating faux DE Tables.## Basic: Returning tables.## Starting DESeq2 pairwise comparisons.## The data should be suitable for EdgeR/DESeq/EBSeq. If they freak out, check the state of the count table and ensure that it is in integer counts.## Choosing the non-intercept containing model.## DESeq2 step 1/5: Including only condition in the deseq model.## converting counts to integer mode## DESeq2 step 2/5: Estimate size factors.## DESeq2 step 3/5: Estimate dispersions.## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## Using a parametric fitting seems to have worked.## DESeq2 step 4/5: nbinomWaldTest.## Starting edgeR pairwise comparisons.## The data should be suitable for EdgeR/DESeq/EBSeq. If they freak out, check the state of the count table and ensure that it is in integer counts.## Choosing the non-intercept containing model.## EdgeR step 1/9: Importing and normalizing data.## EdgeR step 2/9: Estimating the common dispersion.## EdgeR step 3/9: Estimating dispersion across genes.## EdgeR step 4/9: Estimating GLM Common dispersion.## EdgeR step 5/9: Estimating GLM Trended dispersion.## EdgeR step 6/9: Estimating GLM Tagged dispersion.## EdgeR step 7/9: Running glmFit, switch to glmQLFit by changing the argument 'edger_test'.## EdgeR step 8/9: Making pairwise contrasts.## Starting limma pairwise comparison.## libsize was not specified, this parameter has profound effects on limma's result.## Using the libsize from expt$libsize.## Limma step 1/6: choosing model.## Choosing the non-intercept containing model.## Limma step 2/6: running limma::voom(), switch with the argument 'which_voom'.## Using normalize.method=quantile for voom.## Limma step 3/6: running lmFit with method: robust.## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
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## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
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## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
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## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
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## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
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## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
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## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
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## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
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## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
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## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps
## Warning in rlm.default(x = X, y = y, weights = w, ...): 'rlm' failed to
## converge in 20 steps## Limma step 4/6: making and fitting contrasts with no intercept. (~ 0 + factors)## Limma step 5/6: Running eBayes with robust=FALSE and trend=FALSE.## Limma step 6/6: Writing limma outputs.## Limma step 6/6: 1/15: Creating table: mt_st_vs_mt_ex. Adjust=BH## Limma step 6/6: 2/15: Creating table: mt_undef_vs_mt_ex. Adjust=BH## Limma step 6/6: 3/15: Creating table: wt_ex_vs_mt_ex. Adjust=BH## Limma step 6/6: 4/15: Creating table: wt_st_vs_mt_ex. Adjust=BH## Limma step 6/6: 5/15: Creating table: wt_undef_vs_mt_ex. Adjust=BH## Limma step 6/6: 6/15: Creating table: mt_undef_vs_mt_st. Adjust=BH## Limma step 6/6: 7/15: Creating table: wt_ex_vs_mt_st. Adjust=BH## Limma step 6/6: 8/15: Creating table: wt_st_vs_mt_st. Adjust=BH## Limma step 6/6: 9/15: Creating table: wt_undef_vs_mt_st. Adjust=BH## Limma step 6/6: 10/15: Creating table: wt_ex_vs_mt_undef. Adjust=BH## Limma step 6/6: 11/15: Creating table: wt_st_vs_mt_undef. Adjust=BH## Limma step 6/6: 12/15: Creating table: wt_undef_vs_mt_undef. Adjust=BH## Limma step 6/6: 13/15: Creating table: wt_st_vs_wt_ex. Adjust=BH## Limma step 6/6: 14/15: Creating table: wt_undef_vs_wt_ex. Adjust=BH## Limma step 6/6: 15/15: Creating table: wt_undef_vs_wt_st. Adjust=BH## Limma step 6/6: 1/6: Creating table: mt_ex. Adjust=BH## Limma step 6/6: 2/6: Creating table: mt_st. Adjust=BH## Limma step 6/6: 3/6: Creating table: mt_undef. Adjust=BH## Limma step 6/6: 4/6: Creating table: wt_ex. Adjust=BH## Limma step 6/6: 5/6: Creating table: wt_st. Adjust=BH## Limma step 6/6: 6/6: Creating table: wt_undef. Adjust=BH## Comparing analyses 1/15: mt_st_vs_mt_ex## Comparing analyses 2/15: mt_undef_vs_mt_ex## Comparing analyses 3/15: wt_ex_vs_mt_ex## Comparing analyses 4/15: wt_st_vs_mt_ex## Comparing analyses 5/15: wt_undef_vs_mt_ex## Comparing analyses 6/15: mt_undef_vs_mt_st## Comparing analyses 7/15: wt_ex_vs_mt_st## Comparing analyses 8/15: wt_st_vs_mt_st## Comparing analyses 9/15: wt_undef_vs_mt_st## Comparing analyses 10/15: wt_ex_vs_mt_undef## Comparing analyses 11/15: wt_st_vs_mt_undef## Comparing analyses 12/15: wt_undef_vs_mt_undef## Comparing analyses 13/15: wt_st_vs_wt_ex## Comparing analyses 14/15: wt_undef_vs_wt_ex## Comparing analyses 15/15: wt_undef_vs_wt_st## Comparing analyses 1/15: mt_st_vs_mt_ex## Comparing analyses 2/15: mt_undef_vs_mt_ex## Comparing analyses 3/15: wt_ex_vs_mt_ex## Comparing analyses 4/15: wt_st_vs_mt_ex## Comparing analyses 5/15: wt_undef_vs_mt_ex## Comparing analyses 6/15: mt_undef_vs_mt_st## Comparing analyses 7/15: wt_ex_vs_mt_st## Comparing analyses 8/15: wt_st_vs_mt_st## Comparing analyses 9/15: wt_undef_vs_mt_st## Comparing analyses 10/15: wt_ex_vs_mt_undef## Comparing analyses 11/15: wt_st_vs_mt_undef## Comparing analyses 12/15: wt_undef_vs_mt_undef## Comparing analyses 13/15: wt_st_vs_wt_ex## Comparing analyses 14/15: wt_undef_vs_wt_ex## Comparing analyses 15/15: wt_undef_vs_wt_st## Comparing analyses 1/15: mt_st_vs_mt_ex## Comparing analyses 2/15: mt_undef_vs_mt_ex## Comparing analyses 3/15: wt_ex_vs_mt_ex## Comparing analyses 4/15: wt_st_vs_mt_ex## Comparing analyses 5/15: wt_undef_vs_mt_ex## Comparing analyses 6/15: mt_undef_vs_mt_st## Comparing analyses 7/15: wt_ex_vs_mt_st## Comparing analyses 8/15: wt_st_vs_mt_st## Comparing analyses 9/15: wt_undef_vs_mt_st## Comparing analyses 10/15: wt_ex_vs_mt_undef## Comparing analyses 11/15: wt_st_vs_mt_undef## Comparing analyses 12/15: wt_undef_vs_mt_undef## Comparing analyses 13/15: wt_st_vs_wt_ex## Comparing analyses 14/15: wt_undef_vs_wt_ex## Comparing analyses 15/15: wt_undef_vs_wt_st## Comparing analyses 1/15: mt_st_vs_mt_ex## Comparing analyses 2/15: mt_undef_vs_mt_ex## Comparing analyses 3/15: wt_ex_vs_mt_ex## Comparing analyses 4/15: wt_st_vs_mt_ex## Comparing analyses 5/15: wt_undef_vs_mt_ex## Comparing analyses 6/15: mt_undef_vs_mt_st## Comparing analyses 7/15: wt_ex_vs_mt_st## Comparing analyses 8/15: wt_st_vs_mt_st## Comparing analyses 9/15: wt_undef_vs_mt_st## Comparing analyses 10/15: wt_ex_vs_mt_undef## Comparing analyses 11/15: wt_st_vs_mt_undef## Comparing analyses 12/15: wt_undef_vs_mt_undef## Comparing analyses 13/15: wt_st_vs_wt_ex## Comparing analyses 14/15: wt_undef_vs_wt_ex## Comparing analyses 15/15: wt_undef_vs_wt_st## Comparing analyses 1/15: mt_st_vs_mt_ex## Comparing analyses 2/15: mt_undef_vs_mt_ex## Comparing analyses 3/15: wt_ex_vs_mt_ex## Comparing analyses 4/15: wt_st_vs_mt_ex## Comparing analyses 5/15: wt_undef_vs_mt_ex## Comparing analyses 6/15: mt_undef_vs_mt_st## Comparing analyses 7/15: wt_ex_vs_mt_st## Comparing analyses 8/15: wt_st_vs_mt_st## Comparing analyses 9/15: wt_undef_vs_mt_st## Comparing analyses 10/15: wt_ex_vs_mt_undef## Comparing analyses 11/15: wt_st_vs_mt_undef## Comparing analyses 12/15: wt_undef_vs_mt_undef## Comparing analyses 13/15: wt_st_vs_wt_ex## Comparing analyses 14/15: wt_undef_vs_wt_ex## Comparing analyses 15/15: wt_undef_vs_wt_st## Comparing analyses 1/15: mt_st_vs_mt_ex## Comparing analyses 2/15: mt_undef_vs_mt_ex## Comparing analyses 3/15: wt_ex_vs_mt_ex## Comparing analyses 4/15: wt_st_vs_mt_ex## Comparing analyses 5/15: wt_undef_vs_mt_ex## Comparing analyses 6/15: mt_undef_vs_mt_st## Comparing analyses 7/15: wt_ex_vs_mt_st## Comparing analyses 8/15: wt_st_vs_mt_st## Comparing analyses 9/15: wt_undef_vs_mt_st## Comparing analyses 10/15: wt_ex_vs_mt_undef## Comparing analyses 11/15: wt_st_vs_mt_undef## Comparing analyses 12/15: wt_undef_vs_mt_undef## Comparing analyses 13/15: wt_st_vs_wt_ex## Comparing analyses 14/15: wt_undef_vs_wt_ex## Comparing analyses 15/15: wt_undef_vs_wt_stpa_combined <- sm(combine_de_tables(pa_de,
keepers=keepers,
excel=paste0("excel/pa_nobatch-v", ver, ".xlsx")))## Error in merge.data.table(comb, datalst[[i]], by = "row.names", all.x = TRUE): Elements listed in `by` must be valid column names in x and ypa_sig <- extract_significant_genes(pa_combined, lfc=2,
excel=paste0("excel/pa_nobatch_significant-v", ver, ".xlsx"),
according_to="deseq")## Error in extract_significant_genes(pa_combined, lfc = 2, excel = paste0("excel/pa_nobatch_significant-v", : object 'pa_combined' not found## Error in pp(file = "images/sig_barplot.png", image = pa_sig$sig_bar_plots$deseq): object 'pa_sig' not found## Trying attempt: rtracklayer::import.gff3(gff, sequenceRegionsAsSeqinfo=TRUE)## Had a successful gff import with rtracklayer::import.gff3(gff, sequenceRegionsAsSeqinfo=TRUE)## Returning a df with 16 columns and 11946 rows.## The species being downloaded is: Pseudomonas aeruginosa UCBPP-PA14## Error in head(pa_combined$data[[1]], n = 2): object 'pa_combined' not found## # A tibble: 2 x 18
## locusId accession GI scaffoldId start stop strand sysName name
## <int> <chr> <int> <int> <int> <int> <chr> <chr> <chr>
## 1 2194572 YP_78815… 1.16e8 4582 483 2027 + PA14_0… dnaA
## 2 2194573 YP_78815… 1.16e8 4582 2056 3159 + PA14_0… dnaN
## # ... with 9 more variables: desc <chr>, COG <chr>, COGFun <chr>,
## # COGDesc <chr>, TIGRFam <chr>, TIGRRoles <chr>, GO <chr>, EC <chr>,
## # ECDesc <chr>## Error in merge(pa_combined$data[[1]], microbes_annot, by.x = "alias", : object 'pa_combined' not found## Error in eval(expr, envir, enclos): object 'first' not found## Error in colnames(cog_groups) <- c("seqnames", "start", "stop", "strand", : object 'cog_groups' not found## Error in eval(expr, envir, enclos): object 'first' not found## Error in eval(expr, envir, enclos): object 'pa_combined' not found## Error in eval(expr, envir, enclos): object 'wt_stex' not found## Error in eval(expr, envir, enclos): object 'pa_combined' not found## Error in eval(expr, envir, enclos): object 'mt_stex' not found## Error in eval(expr, envir, enclos): object 'pa_combined' not found## Error in eval(expr, envir, enclos): object 'st_wtmt' not found## Error in eval(expr, envir, enclos): object 'pa_combined' not found## Error in eval(expr, envir, enclos): object 'ex_wtmt' not foundextra <- gff_df
extra[["flag"]] <- ""
down_orn <- c("gene1652323", "gene1652325", "gene1652327", "gene1652329", "gene1652331",
"gene1652333", "gene1652335", "gene1652337")
extra[down_orn, "flag"] <- "down_orn"
up_orn <- c("gene1657644", "gene1657646", "gene1657648", "gene1657650", "gene1657652",
"gene1657654", "gene1657656", "gene1657658", "gene1657660", "gene1657662",
"gene1657664", "gene1657666", "gene1657668", "gene1657670", "gene1657672",
"gene1657674", "gene1657676", "gene1657678", "gene1657680", "gene1657682",
"gene1657684", "gene1657686", "gene1657688", "gene1657690", "gene1657692",
"gene1657694", "gene1657696", "gene1657698", "gene1657700", "gene1657702",
"gene1657704", "gene1657706", "gene1657708", "gene1657710", "gene1657712",
"gene1657714")
extra[up_orn, "flag"] <- "up_orn"
effectors <- c("gene1659174", "gene1659176", "gene1650925", "gene1656712")
extra[effectors, "flag"] <- "effectors"
up_other <- c("gene1652095", "gene1652097", "gene1652099", "gene1652101",
"gene1652103", "gene1652105", "gene1652107", "gene1652109",
"gene1652111", "gene1652113", "gene1652115", "gene1652117",
"gene1652119", "gene1652121", "gene1652123", "gene1652125",
"gene1652127", "gene1652129", "gene1652131", "gene1652133",
"gene1652135", "gene1652137", "gene1652139", "gene1652141",
"gene1652143", "gene1652145", "gene1652147", "gene1652149",
"gene1652151", "gene1652153", "gene1652155", "gene1652157",
"gene1652159", "gene1652161", "gene1652163", "gene1652165")
extra[up_other, "flag"] <- "other"
pel <- c("gene1654787", "gene1654789", "gene1654793",
"gene1654795", "gene1654797", "gene1654799")
extra[pel, "flag"] <- "pel"
tile_colors <- c("0000FF", "2222FF", "9999FF", "FF0000", "00FF00")
names(tile_colors) <- c("down_other", "effectors", "other", "pel", "up_orn")
circos_pa13 <- circos_prefix(name="pa14")## This assumes you have a colors.conf in circos/colors/ and fonts.conf in circos/fonts/## It also assumes you have conf/ideogram.conf, conf/ticks.conf, and conf/housekeeping.conf## It will write circos/conf/pa14.conf with a reasonable first approximation config file.## Wrote karyotype to circos/conf/ideograms/pa14.conf## This should match the karyotype= line in pa14.conf## Wrote ticks to circos/conf/ticks_pa14.conf## Warning in file.symlink(from, to): cannot symlink 'conf/pa14.conf' to './
## pa14.conf', reason 'File exists'## Wrote karyotype to circos/conf/karyotypes/pa14.conf## This should match the karyotype= line in pa14.conf## Error in circos_plus_minus(cog_groups, circos_pa13): object 'cog_groups' not found##drops <- wt_stex[["start"]] == "undefined"
##wt_stex <- wt_stex[-drops, ]
##wt_stex[["limma_logfc"]] <- abs(min(wt_stex[["limma_logfc"]])) + wt_stex[["limma_logfc"]]
##pa13_wt_stex <- circos_heatmap(wt_stex, gff_df, colname="limma_logfc",
## cfgout=circos_pa13, basename="wt_stex", outer=pa13_plus)
##drops <- mt_stex[["start"]] == "undefined"
##mt_stex <- mt_stex[-drops, ]
##mt_stex[["limma_logfc"]] <- abs(min(mt_stex[["limma_logfc"]])) + mt_stex[["limma_logfc"]]
##pa13_mt_stex <- circos_heatmap(mt_stex, gff_df, colname="limma_logfc",
## cfgout=circos_pa13, basename="mt_stex", outer=pa13_wt_stex)
pa13_ex_wtmt <- circos_heatmap(ex_wtmt, gff_df, colname="limma_logfc",
cfgout=circos_pa13, basename="ex_wtmt", outer=pa13_plus)## Error in merge(df, annot_df, by = "row.names"): object 'ex_wtmt' not foundpa13_st_wtmt <- circos_heatmap(st_wtmt, gff_df, colname="limma_logfc",
cfgout=circos_pa13, basename="st_wtmt", outer=pa13_ex_wtmt)## Error in merge(df, annot_df, by = "row.names"): object 'st_wtmt' not foundpa13_tiles <- circos_tile(extra, colname="flag", colors=tile_colors,
cfgout=circos_pa13, basename="tile", outer=pa13_st_wtmt)## Writing data file: circos/data/pa14_tileflag_tile.txt with the flag column.## Error in circos_tile(extra, colname = "flag", colors = tile_colors, cfgout = circos_pa13, : object 'pa13_st_wtmt' not foundR version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
locale: LC_CTYPE=en_US.utf8, LC_NUMERIC=C, LC_TIME=en_US.utf8, LC_COLLATE=en_US.utf8, LC_MONETARY=en_US.utf8, LC_MESSAGES=en_US.utf8, LC_PAPER=en_US.utf8, LC_NAME=C, LC_ADDRESS=C, LC_TELEPHONE=C, LC_MEASUREMENT=en_US.utf8 and LC_IDENTIFICATION=C
attached base packages: parallel, stats, graphics, grDevices, utils, datasets, methods and base
other attached packages: edgeR(v.3.22.5), bindrcpp(v.0.2.2), hpgltools(v.2018.11), Biobase(v.2.40.0) and BiocGenerics(v.0.26.0)
loaded via a namespace (and not attached): backports(v.1.1.2), Hmisc(v.4.1-1), fastmatch(v.1.1-0), selectr(v.0.4-1), plyr(v.1.8.4), igraph(v.1.2.2), lazyeval(v.0.2.1), splines(v.3.5.1), BiocParallel(v.1.14.2), GenomeInfoDb(v.1.16.0), ggplot2(v.3.0.0), sva(v.3.28.0), digest(v.0.6.18), foreach(v.1.4.4), htmltools(v.0.3.6), GOSemSim(v.2.6.2), viridis(v.0.5.1), GO.db(v.3.6.0), fansi(v.0.4.0), gdata(v.2.18.0), checkmate(v.1.8.5), magrittr(v.1.5), memoise(v.1.1.0), cluster(v.2.0.7-1), doParallel(v.1.0.14), openxlsx(v.4.1.0), limma(v.3.36.5), readr(v.1.1.1), Biostrings(v.2.48.0), annotate(v.1.58.0), matrixStats(v.0.54.0), enrichplot(v.1.0.2), prettyunits(v.1.0.2), colorspace(v.1.3-2), rvest(v.0.3.2), blob(v.1.1.1), ggrepel(v.0.8.0), dplyr(v.0.7.7), crayon(v.1.3.4), RCurl(v.1.95-4.11), roxygen2(v.6.1.0), genefilter(v.1.62.0), lme4(v.1.1-18-1), bindr(v.0.1.1), survival(v.2.42-6), iterators(v.1.0.10), glue(v.1.3.0), gtable(v.0.2.0), zlibbioc(v.1.26.0), XVector(v.0.20.0), UpSetR(v.1.3.3), DelayedArray(v.0.6.6), scales(v.1.0.0), DOSE(v.3.6.1), DBI(v.1.0.0), Rcpp(v.0.12.19), htmlTable(v.1.12), viridisLite(v.0.3.0), xtable(v.1.8-3), progress(v.1.2.0), units(v.0.6-1), foreign(v.0.8-71), bit(v.1.1-14), preprocessCore(v.1.42.0), Formula(v.1.2-3), stats4(v.3.5.1), htmlwidgets(v.1.3), httr(v.1.3.1), fgsea(v.1.6.0), RColorBrewer(v.1.1-2), gplots(v.3.0.1), acepack(v.1.4.1), pkgconfig(v.2.0.2), XML(v.3.98-1.16), farver(v.1.0), nnet(v.7.3-12), utf8(v.1.1.4), locfit(v.1.5-9.1), labeling(v.0.3), tidyselect(v.0.2.5), rlang(v.0.3.0), reshape2(v.1.4.3), AnnotationDbi(v.1.42.1), munsell(v.0.5.0), tools(v.3.5.1), cli(v.1.0.1), RSQLite(v.2.1.1), devtools(v.1.13.6), ggridges(v.0.5.1), evaluate(v.0.12), stringr(v.1.3.1), yaml(v.2.2.0), knitr(v.1.20), bit64(v.0.9-7), pander(v.0.6.2), zip(v.1.0.0), caTools(v.1.17.1.1), purrr(v.0.2.5), ggraph(v.1.0.2), packrat(v.0.4.9-3), nlme(v.3.1-137), DO.db(v.2.9), xml2(v.1.2.0), biomaRt(v.2.36.1), rstudioapi(v.0.8), compiler(v.3.5.1), pbkrtest(v.0.4-7), curl(v.3.2), variancePartition(v.1.10.3), geneplotter(v.1.58.0), tibble(v.1.4.2), tweenr(v.1.0.0), stringi(v.1.2.4), GenomicFeatures(v.1.32.3), lattice(v.0.20-35), Matrix(v.1.2-14), commonmark(v.1.6), nloptr(v.1.2.1), pillar(v.1.3.0), data.table(v.1.11.8), cowplot(v.0.9.3), bitops(v.1.0-6), corpcor(v.1.6.9), rtracklayer(v.1.40.6), GenomicRanges(v.1.32.7), qvalue(v.2.12.0), colorRamps(v.2.3), latticeExtra(v.0.6-28), R6(v.2.3.0), directlabels(v.2018.05.22), KernSmooth(v.2.23-15), gridExtra(v.2.3), IRanges(v.2.14.12), codetools(v.0.2-15), MASS(v.7.3-50), gtools(v.3.8.1), assertthat(v.0.2.0), SummarizedExperiment(v.1.10.1), DESeq2(v.1.20.0), rprojroot(v.1.3-2), withr(v.2.1.2), GenomicAlignments(v.1.16.0), Rsamtools(v.1.32.3), S4Vectors(v.0.18.3), GenomeInfoDbData(v.1.1.0), mgcv(v.1.8-24), hms(v.0.4.2), clusterProfiler(v.3.8.1), rpart(v.4.1-13), quadprog(v.1.5-5), grid(v.3.5.1), tidyr(v.0.8.1), minqa(v.1.2.4), rmarkdown(v.1.10), rvcheck(v.0.1.1), ggforce(v.0.1.3) and base64enc(v.0.1-3)
## If you wish to reproduce this exact build of hpgltools, invoke the following:## > git clone http://github.com/abelew/hpgltools.git## > git reset b3a13587a9008857c08d9f8b72050762f2fc94bb## This is hpgltools commit: Wed Oct 31 15:26:29 2018 -0400: b3a13587a9008857c08d9f8b72050762f2fc94bbthis_save <- paste0(gsub(pattern="\\.Rmd", replace="", x=rmd_file), "-v", ver, ".rda.xz")
message(paste0("Saving to ", this_save))## Saving to 03_differential_expression_20180718-v20180718.rda.xz