[BioC] Puzzled about limma and PAM results validity

Steve Lianoglou mailinglist.honeypot at gmail.com
Sat Sep 25 22:44:52 CEST 2010

Hi Giulio,

On Sat, Sep 25, 2010 at 8:21 AM, Giulio Di Giovanni
<perimessaggini at hotmail.com> wrote:
> Mhhh, it seems that maybe I wasn't clear, or my previous it passed unnoticed. Please allow me to repost it (see below this email).
> In short: Quite clearly small differentiate genes with Differential Expression. Same results, same genes with PAM, but high CV errors! Is it PAM """failing""", by overestimating the errors (because of the small, even if significative, differences)? Any clues about why I get on one side high misclassification errors for the same genes that on the other side are nicely and clearly differentially expressed?

I'm not sure that your PAM classification result has anything to do
with the validity of the genes that are differentially expressed.

It probably just means that PAM isn't well suited to your problem.
There are likely many reasons for that.


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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