Entering edit mode
Michal Okoniewski
▴
190
@michal-okoniewski-2676
Last seen 10.3 years ago
-----Original Message-----
From: bioconductor-bounces@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