[BioC] Re-mapped Affy CDF files

[James MacDonald]

Has anybody taken a close look at the re-mapped cdf files that the MBNI at the University of Michigan have produced?

http://brainarray.mhri.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp

I find the idea of revisiting the mapping of probes to genes as well as combining the disparate probesets for a given gene into a single probeset appealing, but I think something more than 'Hey that looks like a good idea!' is needed before one could make the case for switching from Affy's cdf to these re-mapped ones. 

Unfortunately, given the fact that there isn't a one-to-one correspondence between the Affy and MBNI probesets, doing a critical comparison of the results is not straighforward. For instance, using the Affy spike-in or GeneLogic dilution datasets won't work AFAIK, since it seems that both Affy and GeneLogic spiked in probe-specific cRNA rather than spiking in full length transcripts for particular genes.

I know of at least one instance where a client was comparing samples with a particular gene 'knocked in' to wild type, and we didn't see any difference when using the Affy CDF but the gene was at the top of the list of significant genes when using an MBNI CDF, so we have some small indication that the MBNI CDFs might be better.

So, does anybody have any experience with these CDFs that might give an indication of their usefulness? Barring that, does anybody have a good way that one could reasonably compare the two probe mappings?

Best,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623



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