[BioC] get probe level intensity from Affymetrix Exon

[shirley zhang]

Hi Raffaele,

Thank you very much. It works.

Shirley

On 3/19/08, raffaele.calogero at unito.it <raffaele.calogero at unito.it> wrote:
> 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
> www:   www.bioinformatica.unito.it
>
>