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Old 01-04-2012, 09:55 PM   #1
Junior Member
Location: LA

Join Date: Nov 2011
Posts: 5
Default Why edgeR ouput some p values larger than 1

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.
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File Type: png Screen shot 2012-01-04 at 10.53.27 PM.png (34.6 KB, 20 views)
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Old 02-01-2013, 03:14 PM   #2
Gordon Smyth
Location: Melbourne, Australia

Join Date: Apr 2011
Posts: 91

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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