In this case, you're in luck. You can find both a .CDF file and a .probe file for this chip: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL1073 Cheers, Cei On Mon, 4 Jun 2007, Jenny Drnevich wrote: > Hi Daniel, > > Also, there's a good chance that you won't be able to use gcrma() on > a custom Affy chip, unless the custom array contains the PM-MM > pairing, and you have a probe file that contains the amount and > location of GC content of the probes, in addition to the cdf file. If > it's a PM only array, you won't be able to do the gc-based background > correction of gcrma, but you can do the model-based background of rma(). > > Cheers, > Jenny > > At 01:50 PM 6/4/2007, Cei Abreu-Goodger wrote: > > >Hi Daniel, > > > >I asked the same a while back. You should start by checking out > >the "makecdfenv" and "matchprobes" vignettes. There should be enough > >information there to get you going. Essentially you have to create your > >own packages for the GNF1M chip and install them. > > > >Cei > > > > > >On Mon, 4 Jun 2007, Daniel Gatti wrote: > > > > > I'm analyzing a publicly available GEO data set (GEO5961) that uses a > > > custom array (GNF1M). The file download from GEO includes a .CDF file > > > for the array, CEL files and several other files that I'm not > > familiar with. > > > > > > > library(gcrma) > > > Loading required package: Biobase > > > Loading required package: tools > > > > > > Welcome to Bioconductor > > > > > > Vignettes contain introductory material. To view, type > > > 'openVignette()' or start with 'help(Biobase)'. For details > > > on reading vignettes, see the openVignette help page. > > > > > > Loading required package: affy > > > Loading required package: affyio > > > Loading required package: matchprobes > > > Loading required package: splines > > > > rawdata = ReadAffy("GSM138562.CEL", "GSM138563.CEL") > > > > norm = gcrma(rawdata) > > > Error in getCdfInfo(object) : Could not obtain CDF environment, problems > > > encountered: > > > Specified environment does not contain gnGNF1Musa > > > Library - package gngnf1musacdf not installed > > > Data for package affy did not contain gngnf1musacdf > > > Bioconductor - gngnf1musacdf not available > > > > > > How can I load the GPL1073.CDF and GPL1073.probe files for the array > > > into the "environment" so that gcrma() can access them? I've tried > > > functions like getCDF(), but it's not clear how to specify a local file > > > as the source. And read.cdffile() reads into an object, but I'm not > > > clear how make that object visible to gcrma(). > > > > > > Thanks, > > > Dan Gatti > > > UNC-CH > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor at stat.math.ethz.ch > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > > >-- > >The Wellcome Trust Sanger Institute is operated by Genome Research > >Limited, a charity registered in England with number 1021457 and a > >company registered in England with number 2742969, whose registered > >office is 215 Euston Road, London, NW1 2BE. > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor at stat.math.ethz.ch > >https://stat.ethz.ch/mailman/listinfo/bioconductor > >Search the archives: > >http://news.gmane.org/gmane.science.biology.informatics.conductor > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich at uiuc.edu > > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.