[BioC] fisher exact test pairwise comparisons

Steve Lianoglou mailinglist.honeypot at gmail.com
Fri Mar 9 00:10:08 CET 2012


On Thu, Mar 8, 2012 at 5:36 PM, Ann Loraine <aloraine at gmail.com> wrote:
> Hi,
> I'm also interested in this question.
> How would you recommend handling replicates?
> For example, if you had counts for each of three control samples and
> each of three treatments, would it make sense to run "sage.test" for
> every combination,  get a p value for each test, and then combine them
> somehow?

You might consider using something like edgeR or DESeq for the use
cases you're probably thinking about ...


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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