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12102013, 11:03 PM  #1 
Member
Location: ca Join Date: Oct 2012
Posts: 11

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! 
12312015, 08:08 AM  #2 
Junior Member
Location: Houston USA Join Date: Mar 2014
Posts: 9

Have you found the answer? I am also curious. Thank you!

01022016, 07:47 AM  #3 
Member
Location: P Join Date: Apr 2014
Posts: 18

Do you need CPM per each sample after TMM normalization?
you could do something like this cpm < cpm(d, log=TRUE, lib.sizes=lib.sizes, normalized.lib.sizes = TRUE, prior.count=0.25) if your cpm values are negative then you can set the prior.count to a different value 
01042016, 08:08 AM  #4 
Junior Member
Location: Houston USA Join Date: Mar 2014
Posts: 9

Thank you! But we meant mean values for each group/condition.

08282018, 08:06 AM  #5 
Junior Member
Location: Ohio, USA Join Date: Aug 2018
Posts: 1

Manual Calc option
So, I know it isn't ideal, but let's take the actual values of log(CPM) and log(FC) that you have from edgeR. Keep in mind this will only work if your replicates of experimental and control were equal, but you could tweak it as needed. Might be worth double checking that logCPM is using base 2 which I believe is default.
Using "A" to be the average expression of your experimental condition and "B" to be your control as you've run it. FC=A/B, so 2^log(FC) will get you (A/B) CPM=(A+B)/2, so 2^log(CPM)=(A+B)/2 Basic algebra solves for B, B=2(2^log(CPM))/(1+2^(log(FC))) and then A= 2(2^log(CPM))  B Using the values of a typical EdgeR, this is minimal R work to generate the columns you wanted. Hope this helps! 
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edger, rnaseq 
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