Hi,
I am using edgeR for some RNASeq analysis. My question concerns the DGEList function and its "group" parameter. I realized that, whether doing group=mydesignfactor or group=rep(1,ncol(counts)), the cpm numbers that I get after
counts.TMM <- calcNormFactors(counts.DGEList)
cpm.TMM=cpm(counts.TMM, normalized.lib.sizes=TRUE)
are strictly identical in either case. The only difference between both ways is that the counts.TMM$samples$group column duly reflects what I put in in "group".
Is this normal? What is it that I am missing? Is the "group" nevertheless taken into account on the subsequent estimateGLMCommonDisp, estimateGLMTrendDisp, estimateGLMTagDisp, glmFit, glmLRT etc.?
Thanks in advance for your help.
Best,
David Rengel
I am using edgeR for some RNASeq analysis. My question concerns the DGEList function and its "group" parameter. I realized that, whether doing group=mydesignfactor or group=rep(1,ncol(counts)), the cpm numbers that I get after
counts.TMM <- calcNormFactors(counts.DGEList)
cpm.TMM=cpm(counts.TMM, normalized.lib.sizes=TRUE)
are strictly identical in either case. The only difference between both ways is that the counts.TMM$samples$group column duly reflects what I put in in "group".
Is this normal? What is it that I am missing? Is the "group" nevertheless taken into account on the subsequent estimateGLMCommonDisp, estimateGLMTrendDisp, estimateGLMTagDisp, glmFit, glmLRT etc.?
Thanks in advance for your help.
Best,
David Rengel
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