[BioC] How to use DESeq to normalize and estimate variance in a RNAseq timecourse analysis

[Simon Anders]

Hi Marie

> In our dataset, we tried both procedure and we do see a difference in
> the DESeq output. Maybe, as you said, the  estimation of dispersion is
> the same for both procedures, but the normalization step (estimation of
> size Factors ) gives different outputs when using complete or partial
> tables (with only a subset of the samples)?

yes, this could be, but I'd be surprised if it make much of a difference 
in the test outcomes. If you are still worried about the issue, maybe 
post some detilas. What size factors do you get using only one time 
point at a time and what do you get using all of them together? Can you 
find an example for a gene where you see an appreciable difference in 
the p value? If so, are the dispersion estimates the same?

   Simon