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).

Thanks!

Nick

	[[alternative HTML version deleted]]

