[BioC] How to use DESeq to normalize and estimate variance in a RNAseq timecourse analysis
anders at embl.de
Thu May 10 11:40:13 CEST 2012
> 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?
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