[BioC] use of huex10stv2cdf_1.15.0.tar.gz and human exon array analysis

[Michal Okoniewski]

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch on behalf of Dan Strumpf
Sent: Mon 1/26/2009 10:17 PM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] use of huex10stv2cdf_1.15.0.tar.gz and human exon array analysis
 
Hello,

I am new to exon array analysis and have used the huex10stv2cdf_1.15.0.tar.gz 
package (downloaded from 
http://aurora.lbl.gov/static/huex10stv2cdf_1.15.0.tar.gz
)as a cdf source/mapping for processing Human exon array data within 'affy' 
package. Processing went smoothly without any error messages. Noticed some 
communication about this package in Oct. 2007, and am not clear if results 
using it are relaible.
I am interested in processing Human exon array data also with gcRMA and am 
wondering if should use the above package or use xps/exonmap/oligo instead? 
Would like to know also what are to options for differential expression 
analysis equivalent to samr limma or RankProd for paired samples from within 
exon array analysis packages or could the preprocessed/normalized data be 
exported and used with xps/exonmap/oligo packages.

Thanks,

Dan
=====================================================

Hi Dan,

xps uses the "most proper" pgf and bkg Affymetrix annotation, while exonmap gives you
more flexibility of playing around with annotations - both require extra database installation
effort, but I think it is worth it.

Did you run the summarization with this package? I think the discussion in Oct 07 was about
the fact that you have to remove some probesets to run RMA... or was it fixed?
You can use also the CDFs from X:MAP downloads page - they manage with RMA/plier.

Cheers,
Michal