[BioC] edgeR problem

Hayssam Soueidan h.soueidan at nki.nl
Tue Feb 26 23:01:20 CET 2013


Hi Nima,


I never had such high value for the BCV. In my analysis (mouse and human RNA-Seq), the BCV is usually way below 1. From the name of your data file, it looks like you have normalized FPKM data. EdgeR expect raw counts data (integers). That might be causing problems. Could you provide a head of your data.TMM data.frame? 
Further could you 1) provide a session.info and 2) provide some of the warnings? 

Regards,
Sam.

On Feb 26, 2013, at 4:39 PM, Nima Rafati <nimarafati at gmail.com> wrote:

> 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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> 
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