[BioC] Human exon array chip

[James W. MacDonald]

Hi Matt,

Matthew Walker wrote:
> I am having trouble reading a human exon array chip using the  
> affylmGUI software. The program cannot find the HuEx-l_OST-V2 file,  
> although I have it downloaded. I am a new user to R and microarrays  
> in general. Please let me know if there is anyway to use the software  
> with the Human exon array.

The affylmGUI software is not designed to work directly with the raw 
exon chip data. Your closest bet would be to use the oligo package. 
However, the oligo package is still under development so is probably not 
the best place for a new R user to start. In addition, the oligo package 
will require you to make a PDEnv with the HuEx-l_OST-V2.cdf file, which 
I am unable to do on a 64 bit Linux box with 8 Gb RAM (I think 16 Gb is 
sufficient).

Probably your best bet would be to get Affy's Exact software and use 
that to compute expression values for each probeset (exon), and then 
import those data into R. This will still require a reasonably large 
amount of RAM, and will likely be easier to do on a *nix variant (you 
don't mention your OS).

Other options would include buying some commercial software like 
Genomatix or XRAY, etc. See here for some choices:

http://www.affymetrix.com/products/software/compatible/exon_expression.affx

Best,

Jim


> 
> Matt Walker
> mattw at uchicago.edu
> University of Chicago
> Geof Greene Lab
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
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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