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

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 > >