[BioC] DESeq variance stabilization

Steve Lianoglou mailinglist.honeypot at gmail.com
Sun Aug 26 15:12:30 CEST 2012


On Sun, Aug 26, 2012 at 8:19 AM, Lana Schaffer <schaffer at scripps.edu> wrote:
> Steve,
> Thank you for your suggestion.   However, the idea of these datasets
> Is to access the reproducability of the results.

So ... are they reproducible? :-)

You only mentioned that one of your datasets has "lower standard
deviation" and a longer set of differentially expressed genes -- but I
guess that would stand to reason, no?

Is your assessment of reproducibility strictly a function of the sets
of genes called differentially expressed in the two scenarios?

If so, is the overlap of the called genes between the two sets
particularly poor?

How about looking at some type of rank correlation between the two
sets of "up" and "down" genes? Perhaps you can look at the top 10, 20,
50, etc. sets of genes and compare like so.

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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