edgeR
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@da307361
Last seen 3 days ago
Turkey

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?

rnaseq edgeR • 147 views
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@gordon-smyth
Last seen 1 hour ago
WEHI, Melbourne, Australia

The documentation shows that you should use:

topTags(et)

The output not only includes FDR values but also ranks the genes in order of DE significance.

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