the cdf env is already there. http://www.bioconductor.org/data/metaData.html what is still missing is the probe sequence info package. we are working on that... On Wed, 27 Aug 2003, James MacDonald wrote: > You will have to use the makecdfenv package to make a cdf environment > that affy can use. See the help for makecdfenv. > > Jim > > > > James W. MacDonald > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > >>> "laurent buffat" <laurent.buffat@it-omics.com> 08/27/03 10:32AM > >>> > > Dear all, > > Affymetrix provied a new SpikeIn data Sets > https://www.affymetrix.com/support/datasets.affx > > But, this data sets requires a special, alternate chip description > file > (CDF), > because there is eight artificial clones > > And when I try to load/bg correct and normalise the data in R, I have > an > error at the bg.correct step : > > > exp <- ReadAffy(filenames=list.cel,phenoData=phenodata,verbose=T) > Ok, no problem > > > exp <- bg.correct(exp, method = "rma",verbose=T) > > Sample : 1Error in .local(object, ...) : Information about probe > locations > for unknown could not be found. > Try downloading the unknowncdf package from > http://www.bioconductor.org/data/cdfenvs/cdfenvs.html > > > The correct CDF is available at affymetrix. > I have try to put this CDF in the data directory (as it was necessary > in the > first version of affy), but it doesn' work. > > How I can read this data with affy ? > > Thanks for your help. > > L. Buffat > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

Hi, Thanks a lot. It's work. Laurent Buffat -----Message d'origine----- De : Crispin Miller [mailto:CMiller@PICR.man.ac.uk] Envoy? : mercredi 27 ao?t 2003 16:56 ? : laurent buffat; bioconductor@stat.math.ethz.ch Objet : RE: [BioC] New Affy SpikeIn Data Set & Affy Hi, It looks like you need to download the hgu133atagcdf data set from www.bioconductor.org After you've run ReadAffy, you probably need to set the cdf name to "hgu133atag" i.e. eset <- ReadAffy(...); eset@cdfName <- "hgu133atag" eset.rma <- rma(eset) ... or whatever. Hope that helps! Crispin > -----Original Message----- > From: laurent buffat [mailto:laurent.buffat@it-omics.com] > Sent: 27 August 2003 15:33 > To: bioconductor@stat.math.ethz.ch > Subject: [BioC] New Affy SpikeIn Data Set & Affy > > > > Dear all, > > Affymetrix provied a new SpikeIn data Sets > https://www.affymetrix.com/support/datasets.affx > > But, this data sets requires a special, alternate chip > description file > (CDF), > because there is eight artificial clones > > And when I try to load/bg correct and normalise the data in > R, I have an > error at the bg.correct step : > > > exp <- ReadAffy(filenames=list.cel,phenoData=phenodata,verbose=T) > Ok, no problem > > > exp <- bg.correct(exp, method = "rma",verbose=T) > > Sample : 1Error in .local(object, ...) : Information about > probe locations > for unknown could not be found. > Try downloading the unknowncdf package from > http://www.bioconductor.org/data/cdfenvs/cdfenvs.html > > > The correct CDF is available at affymetrix. > I have try to put this CDF in the data directory (as it was > necessary in the > first version of affy), but it doesn' work. > > How I can read this data with affy ? > > Thanks for your help. > > L. Buffat > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > -------------------------------------------------------- This email is confidential and intended solely for the use o...{{dropped}}