thank you!
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biology_inform •
edgeR
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?
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Gordon Smyth
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biology_inform •
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biology_inform •
1 answer
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.
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