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idyll_ty 01-04-2012 09:55 PM

Why edgeR ouput some p values larger than 1
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I was using edgeR to do differential expression on a RNA-seq dataset, but when I check the p.value distribution of the output, I found ~700 genes got a p value larger than 1... Just wondering if anyone else got this problem before? And why I got such a weird a result. Here's my codes,

d <- DGEList(counts=countsTable, group=conds, lib.size = lib.sizes) #I used the raw read counts as instructed
d <- calcNormFactors(d, method="TMM")
d <- estimateCommonDisp(d)
et.commonDis <- exactTest(d)

hist(et.commonDis$table$p.value, breaks=100, col="skyblue", border="slateblue", main="pval distribution_edgeR")

I got a picture as attached...

May I have your ideas? Thanks.

Gordon Smyth 02-01-2013 03:14 PM

edgeR doesn't produce p-values greater than one. If you did observe this, then it would be a bug in the software, and you should write to the authors, who always appreciate being alerted to such things. But make sure first you are using the current software and that you can reproduce the problem.

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