[Bioc-sig-seq] RNASeq, differential expression between group, and large variance within groups

[Laurent Gautier]

Thanks to Mads, Simon, and Steve.

In summary:

- extreme variance within group (zero or large value) is not a good 
sign, and experimental issues are to be suspected
- pooling (summing) tags over reference transcripts can rescue some of 
the signal
- DESeq, and to some extent edgeR, will report as differentially 
expressed such gene/tags with such pathological counts while they should 
not. The issue is acknowledged and care should be taken (here we use 
various visualizations to complement the p-values).




Laurent