[BioC] DESeq variance stabilization

[Steve Lianoglou]

Hi,

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?

HTH,
-steve

-- 
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