[BioC] Re-mapped Affy CDF files

James W. MacDonald jmacdon at med.umich.edu
Wed Jan 11 15:51:38 CET 2006

Sean Davis wrote:
> I'm not sure what their build process is, but doesn't Ensembl do some
> probe-based mappings?

Maybe. I couldn't find anything obvious in a cursory glance at their 

Anyway, the main question for me is not the number or type of 
alternative mappings that exist for Affy arrays (there are 19 different 
CDFs that the MBNI folks produce, including several based on Ensembl 
mappings). I am more concerned with being able to establish a defensible 
rationale for using a particular mapping.

I guess what we do right now with the Affy CDFs isn't defensible except 
on a historical basis, but the weight of history is pretty strong. For 
instance, attributing significance at an alpha of < 0.05 has no 
rationale AFAIK, but is pretty much written in stone due to precedent.

OTOH, most if not all microarray data are caveat emptor - it is 
incumbent on the end user to take the magical list of differentially 
expressed genes and validate them with an alternative methodology.

Given that state of affairs, is it not reasonable to choose the probe 
mappings that one uses with the same logic that one uses for choosing 
the preferred way of computing expression values?


> Sean

James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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