index.html 01_annotation.html 02_estimation_macrophage.html
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.
For the moment, I will assume we only want to deal with the 8 samples. However, I will try a count-filtered run, an annotation filtered run, and both.
keepers <- list(
"embryo" = c("embryogenic", "nonembryogenic"))
k8tx_count_de <- all_pairwise(k8tx_count, parallel=FALSE)## Error in normalize_expt(input, filter = TRUE, batch = FALSE, transform = "log2", : object 'k8tx_count' not foundk8tx_count_tables <- combine_de_tables(k8tx_count_de, keepers=keepers,
excel=paste0("excel/k8_count_de_tx-v", ver, ".xlsx"),
sig_excel=paste0("excel/k8_count_sig_tx-v", ver, ".xlsx"))## Error in combine_de_tables(k8tx_count_de, keepers = keepers, excel = paste0("excel/k8_count_de_tx-v", : object 'k8tx_count_de' not foundk8tx_conf_de <- all_pairwise(k8tx_conf)## Error in normalize_expt(input, filter = TRUE, batch = FALSE, transform = "log2", : object 'k8tx_conf' not foundk8tx_conf_tables <- combine_de_tables(k8tx_conf_de, keepers=keepers,
excel=paste0("excel/k8_conf_de_tx-v", ver, ".xlsx"),
sig_excel=paste0("excel/k8_conf_sig_tx-v", ver, ".xlsx"))## Error in combine_de_tables(k8tx_conf_de, keepers = keepers, excel = paste0("excel/k8_conf_de_tx-v", : object 'k8tx_conf_de' not foundk8tx_conf_count_de <- all_pairwise(k8tx_conf_count)## Error in normalize_expt(input, filter = TRUE, batch = FALSE, transform = "log2", : object 'k8tx_conf_count' not foundk8tx_conf_count_tables <- combine_de_tables(k8tx_conf_count_de_tx, keepers=keepers,
excel=paste0("excel/k8_conf_count_de_tx-v", ver, ".xlsx"),
sig_excel=paste0("excel/k8_conf_count_sig_tx-v", ver, ".xlsx"))## Error in combine_de_tables(k8tx_conf_count_de_tx, keepers = keepers, excel = paste0("excel/k8_conf_count_de_tx-v", : object 'k8tx_conf_count_de_tx' not foundindex.html sample_estimation.html
pander::pander(sessionInfo())R version 3.4.4 RC (2018-03-09 r74380)
**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: stats, graphics, grDevices, utils, datasets, methods and base
other attached packages: hpgltools(v.2018.03)
loaded via a namespace (and not attached): Rcpp(v.0.12.15), pillar(v.1.2.1), compiler(v.3.4.4), plyr(v.1.8.4), base64enc(v.0.1-3), iterators(v.1.0.9), tools(v.3.4.4), digest(v.0.6.15), evaluate(v.0.10.1), memoise(v.1.1.0), tibble(v.1.4.2), gtable(v.0.2.0), rlang(v.0.2.0), foreach(v.1.4.4), commonmark(v.1.4), yaml(v.2.1.18), parallel(v.3.4.4), withr(v.2.1.1), stringr(v.1.3.0), knitr(v.1.20), roxygen2(v.6.0.1), xml2(v.1.2.0), devtools(v.1.13.5), rprojroot(v.1.3-2), grid(v.3.4.4), data.table(v.1.10.4-3), Biobase(v.2.38.0), R6(v.2.2.2), rmarkdown(v.1.9), pander(v.0.6.1), ggplot2(v.2.2.1), magrittr(v.1.5), scales(v.0.5.0), backports(v.1.1.2), codetools(v.0.2-15), htmltools(v.0.3.6), BiocGenerics(v.0.24.0), colorspace(v.1.3-2), stringi(v.1.1.7), lazyeval(v.0.2.1) and munsell(v.0.4.3)
message(paste0("This is hpgltools commit: ", get_git_commit()))## If you wish to reproduce this exact build of hpgltools, invoke the following:## > git clone http://github.com/abelew/hpgltools.git## > git reset e3a7f13d63d6906d825dbfad37273ddd71e44e86## R> packrat::restore()## This is hpgltools commit: Mon Mar 12 12:11:17 2018 -0400: e3a7f13d63d6906d825dbfad37273ddd71e44e86this_save <- paste0(gsub(pattern="\\.Rmd", replace="", x=rmd_file), "-v", ver, ".rda.xz")
message(paste0("Saving to ", this_save))## Saving to 03_differential_expression_tx-v20171102.rda.xztmp <- sm(saveme(filename=this_save))