[BioC] DESeq variance stabilization

[Lana Schaffer]

Steve,
Thank you for your suggestion.   However, the idea of these datasets
Is to access the reproducability of the results.
Lana

-----Original Message-----
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

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