[BioC] DESeq variance stabilization
schaffer at scripps.edu
Sun Aug 26 14:19:15 CEST 2012
Thank you for your suggestion. However, the idea of these datasets
Is to access the reproducability of the results.
From: Steve Lianoglou [mailto:mailinglist.honeypot at gmail.com]
Sent: Sunday, August 26, 2012 5:18 AM
To: Lana Schaffer
Cc: bioconductor at r-project.org
Subject: Re: [BioC] DESeq variance stabilization
On Sun, Aug 26, 2012 at 7:24 AM, Lana Schaffer <schaffer at scripps.edu> wrote:
> 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?
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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