[BioC] Affy EXON Array: iterPLIER or RMA

James W. MacDonald jmacdon at med.umich.edu
Tue May 8 18:44:01 CEST 2007

Daniel Brewer wrote:
> I did look into exonmap, but was scared off by the memory (mainly) and
> setup requirements.  Is it possible to use APT (affymetrix power tools)
> to produce the exon-level summaries and then use the exonmap package for
> the annotation and analysis?  The advantages to using APT is that it
> uses memory efficient techniques in C++ unlike R.

I suppose you could, but that sort of misses the whole point of the 
exonmap package, which I think is to be able to choose which probesets 
you want to use when computing an expression value for a particular gene.

The annotation will probably not be much different from what you get 
using Affy's software (at the level of expression values for a set of 
probesets), so in this instance I don't know if you gain much for the 
outlay of time.



> Many thanks
> Dan

James W. MacDonald, M.S.
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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