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 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
