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Old 01-31-2014, 05:13 AM   #1
Location: UK

Join Date: Jun 2011
Posts: 61
Default edgeR: fold change reported by exactTest for zero values of rna-seq

I have used the exact test in edgeR to compute the log fold changes. Here is the snippet:

d <- DGEList(counts=counts, group=samples$Condition)
d <- calcNormFactors(d)
d <- estimateCommonDisp(d)
d <- estimateTagwiseDisp(d)
de <- exactTest(d)
I've noticed that some genes have zero expression in all samples belonging to one of the two conditions. This would make the fold change mathematically undefined (division by zero). Yet the FC is reported as being ~2^-9. My question is - how does edgeR come up with this value? I've checked both the manual and the reference guide but couldn't figure out. There are various functions that accept pseudocounts as parameters but I have entered none in my snippet. So how does edgeR make up for the zero values in this particular case (which seems to be the default usage of the exactTest)?
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