index.html

rpoe <- set_expt_colors(rpoe)
rpoe_metrics <- sm(graph_metrics(rpoe))
rpoe_norm <- sm(normalize_expt(rpoe, transform="log2", convert="cpm", norm="quant", filter=TRUE))
rpoe_norm_metrics <- sm(graph_metrics(rpoe_norm))

rpoe_metrics$libsize

## mouset48r2 is low, rpoet0 is high  They are not tragic
rpoe_metrics$density

## Ok, I am a bit concerned about the 48 hour data
rpoe_norm_metrics$corheat

## Warning in doTryCatch(return(expr), name, parentenv, handler): "title" is not a
## graphical parameter

## Warning in doTryCatch(return(expr), name, parentenv, handler): "title" is not a
## graphical parameter

## Warning in doTryCatch(return(expr), name, parentenv, handler): "title" is not a
## graphical parameter

## t0 is brightest pink, t12 is 2nd brightest, t24 starting to get brown, t48 is brownish
## There is some funky batch effect going on which we will need to address
## Yoann wants colors:  t0='red', t12='orange', t24='yellow', t48='green'
rpoe_norm_metrics$pc_plot

## the one 24 hour sample is a bit of an arsehole
rpoe_norm_metrics$smc

## t24 m2v2

Small query from Dr. McIver

Can we do a PCA of just the wt/mutant samples?

sub <- subset_expt(rpoe, subset="condition!='rpoe_comp'")

## subset_expt(): There were 12, now there are 8 samples.

sub_norm <- normalize_expt(sub, transform="log2", convert="cpm", norm="quant", filter=TRUE)

## Removing 66 low-count genes (1748 remaining).

plot_pca(sub_norm)$plot

## First try a normal condition + batch model
ver <- "202112"
sub_pairwise <- all_pairwise(sub)

## Plotting a PCA before surrogate/batch inclusion.

## Using limma's removeBatchEffect to visualize with(out) batch inclusion.

## Finished running DE analyses, collecting outputs.

## Comparing analyses.

keepers <- list(
    "mut_wt" = c("rpoe_mut", "rna_ll"))
sub_tables <- combine_de_tables(sub_pairwise, keepers=keepers,
                                extra_annot=exprs(sub_norm),
                                excel=paste0("excel/rpoe_nocomplement_tables-v", ver, ".xlsx"),
                                sig_excel=paste0("excel/rpoe_nocomplement_sig-v", ver, ".xlsx"),
                                abundant_excel=paste0("excel/rpoe_nocomplement_abundant-v", ver, ".xlsx"))

## Deleting the file excel/rpoe_nocomplement_tables-v202112.xlsx before writing the tables.

## Error in is.nan(tmp) : default method not implemented for type 'list'

## Deleting the file excel/rpoe_nocomplement_sig-v202112.xlsx before writing the tables.

## Error in is.nan(tmp) : default method not implemented for type 'list'

## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'

## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'

## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'

## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'

## Error in is.nan(tmp) : default method not implemented for type 'list'

## Deleting the file excel/rpoe_nocomplement_abundant-v202112.xlsx before writing the tables.

## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'

The original contrasts

rpoe_pairwise <- all_pairwise(rpoe)

## Plotting a PCA before surrogate/batch inclusion.

## Using limma's removeBatchEffect to visualize with(out) batch inclusion.

## Finished running DE analyses, collecting outputs.

## Comparing analyses.

keepers <- list(
    "mut_wt" = c("rpoe_mut", "rna_ll"),
    "comp_wt" = c("rpoe_comp","rna_ll"),
    "mut_comp" = c("rpoe_mut", "rpoe_comp"))
rpoe_tables <- combine_de_tables(rpoe_pairwise, keepers=keepers,
                                 extra_annot=exprs(rpoe_norm),
                                 excel=paste0("excel/rpoe_tables-v", ver, ".xlsx"),
                                 sig_excel=paste0("excel/rpoe_sig-v", ver, ".xlsx"),
                                 abundant_excel=paste0("excel/rpoe_abundant-v", ver, ".xlsx"))

## Warning in if (table_names == 0) {: the condition has length > 1 and only the
## first element will be used

## Error in is.nan(tmp) : default method not implemented for type 'list'

## Error in is.nan(tmp) : default method not implemented for type 'list'

## Error in is.nan(tmp) : default method not implemented for type 'list'

## Error in is.nan(tmp) : default method not implemented for type 'list'

## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'

## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'

## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'

## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'

## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'

## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'

## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'

## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'

## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'

## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'

## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'

## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'

## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'

## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'

## Error in is.nan(tmp) : default method not implemented for type 'list'

## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'
## Error in is.nan(tmp) : default method not implemented for type 'list'

RNA/TNSeq of S.pyogenes 5448: rpoE influence on gene expression

atb abelew@gmail.com

2021-12-07

Small query from Dr. McIver

The original contrasts