[BioC] get probe level intensity from Affymetrix Exon

[raffaele.calogero at unito.it]

You can do it using one of the programs available in
apt-tools from affymetrix
(http://www.affymetrix.com/support/developer/powertools/index.affx):
apt-cel-extract will extract probe level intensities from
cel files.
This program memory maps all the cel files from which
intensities will be extracted. As a result, there is an
upper limit on the number of cel files that can be
extracted at the same time. The practical limit appears to
be 25 cel files on a Windows XP 32-bit computer with 2Gb
of memory.

apt-cel-extract -o out.txt [-c chip.clf -p chip.pgf] [-d
chip.cdf] \
  --probeset-ids=norm-exon.txt
--probeset-ids=norm-intron.txt \
  --probe-ids=antigenomic.bgp *.cel

Hope it helps
Raffaele


shirley zhang wrote:
> > Dear Bioconductor,
> >
> >  I usually obtain exon-level/gene-level signal using
Plier/RMA
> > implemented in Affymetrix's Expression Console,
however there is no
> > way to get probe level intensity from it. Does anybody
know how to get
> > probe level intensity from Affymetrix Exon Array
platform?
> >
> > Thanks,
> > Shirley
> >

----------------------------------------
Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
Dipartimento di Scienze Cliniche e Biologiche
c/o Az. Ospedaliera S. Luigi
Regione Gonzole 10, Orbassano
10043 Torino
tel.   ++39 0116705417
Lab.   ++39 0116705408
Fax    ++39 0119038639
Mobile ++39 3333827080
email: raffaele.calogero at unito.it
       raffaele[dot]calogero[at]gmail[dot]com
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