edgeR: how to calculate group average/means ?
I am trying edgeR now to find deferentially expressed genes.
I have run
d < DGEList(counts=data,group=g,lib.size=libSizes)
d < calcNormFactors(d)
d < estimateCommonDisp(d)
d < estimateTagwiseDisp(d)
d < exactTest(d)
# d.final < topTags(de.com,n = length(data[,1]))
and got some results like
logFC logCPM PValue
A1bg 1.168034660 3.842894 0.4137326
A1cf 0.000000000 Inf 1.0000000
A1i3 0.000000000 Inf 1.0000000
A2m 0.003703085 4.419204 0.9421192
A3galt2 0.437990409 2.861665 0.2611483
But I'd like to know the average/mean of the gene expressions in each condition/groups?
It seems logFC it is different from "log2(rowMeans(GrpB)/ rowMeans(GrpA))" calculating from cpm() counts.
How should I do the calculation ?
Thanks!
