Dear all,

I have RNA-seq libraries of 12 individuals in two groups (6 replicates
each). I would like to do differential expression analyses using a GLM with
effect of group and sex on the transcripts. I followed the manual and in
last step for calculation of dispersion (estimateGLMCommonDisp)  I received
a high value with a warning. Here comes all commands that I have used:

data.TMM<-read.table("Mod-H-transcripts.ount.matrix.TMM_normalized.FPKM",row.names=1,header=T)
sex<-factor(c("M","F","M","F","M","F","M","F","M","F","F","M"))
grp<-factor(c("W","W","W","W","W","W","D","D","D","D","D","D"))
y.TMM<-DGEList(count=data.TMM.new,group=group.D.W)
data.frame(Sample=colnames(y.TMM),grp,sex)
design<-model.matrix(~grp+sex)
rownames(design)<-colnames(y.TMM)
y.TMM <- estimateGLMCommonDisp(y.TMM, design, verbose=TRUE)

Disp = 3.99994 , BCV = 2
There were 50 or more warnings (use warnings() to see the first 50)

Despite of error, is the generated dispersion reliable? can I continue with
analyses?
Best regards,
Nima

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