[BioC] compare expression measures (and AffyComp)

Sean Davis sdavis2 at mail.nih.gov
Mon Jan 9 21:02:43 CET 2006

On 1/9/06 2:47 PM, "Mohammad Esad-Djou" <shahrgol at web.de> wrote:

> Thank you for your antwort.
> I would like to discuss more second question.
>>> 2. And which mathematical methods for comparison between preprocessing can I
>>> use? 
>> One place to look would be the affycomp package.  However, you might want to
>> look at the literature a bit before going too far; some of these comparisons
>> have been done already with tightly controlled experiments.
> I worked before with AffyComp, but the package is not sufficient flexibly.
> In addition there are limited static information (Assessment summary
> statistics table) with certain preprocessing methods (MAS, dChip, RMA).
> simply said, I want more than median SD, R2, correlation, etc.. and I look for
> meaningful Literature and source about the problem.

Since affycomp is open source, you can certainly extend their methods with
whatever measures you like.  However, I think you need to know what measures
you want to use and what your goals are.


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