[BioC] DESeq variance stabilization

Steve Lianoglou mailinglist.honeypot at gmail.com
Sun Aug 26 14:18:06 CEST 2012


On Sun, Aug 26, 2012 at 7:24 AM, Lana Schaffer <schaffer at scripps.edu> wrote:
> Hi,
> I have 2 RNAseq datasets which are the same experiment both having 8 control and 8 treated
> Samples.  I found that they have slightly different standard deviation values and that the
> Results are different between the 2 datasets.  The set with the lower standard deviation
> Gives a longer list of high adj.pvalues.   Can you give me any help here?

You could try to include the batch as a covariate in your design and
run all 16 controls vs 16 treated samples in one go.

Is that the type of help you are looking for, or?


Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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