edgeR

Question

[biology_inform]

Hi, in edgeR how can I write the FDR values to DE file?

et <- exactTest(dgelist)
fdr <- p.adjust(et$table$PValue, method="BH")

I know exactTest doesnt produce FDR values but with fdr <- p.adjust(et$table$PValue, method="BH") i think i am calculating fdr values but how can I include them to DE file?

[Gordon Smyth]

Cross posted to Bioconductor https://support.bioconductor.org/p/9143614/

Answer 1

[ATpoint]

Please read the manual: https://www.bioconductor.org/packages/devel/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf

Section 2.10.2 convers the exact test and advises to use topTags() after the exactTest which takes care of the FDR. edgeR is an end-to-end software for differential analysis, you don't need to come up with custom code, especially not for these trivial things.

[biology_inform]

thank you!