Hi Ewy. Just to follow up on Laurent's post. I'm afraid I can't speak to the problems you are having below ... but I do know of at least 3 ways to preprocess Gene 1.0 ST data (say, with RMA) in R: 1. aroma.affymetrix http://groups.google.com/group/aroma-affymetrix/web/mogene-1-0-st-v1 (can follow mostly the same steps as in http://groups.google.com/group /aroma-affymetrix/web/human-exon-array-analysis) 2. xps package https://stat.ethz.ch/pipermail/bioconductor/2008-May/022267.html 3. as you were doing, perhaps spelled out a little better at (+ using 'rma' in the oligo package): http://article.gmane.org/gmane.science.biology.informatics.conductor/1 8963/ HTH, Mark On 06/11/2008, at 5:24 PM, laurent wrote: > Hi Mathe, > > For historical reasons, the "annotation" is the association between > probe sets and gene name, chromosomal location, etc... > The CDF data structure models the files with extension .cdf (Chip > Definition File), and contains the association between probe position > on the array and the probe set the probe belongs to. > > This earlier post is related to the problem you are having: > https://stat.ethz.ch/pipermail/bioconductor/2007-November/020188.html > > > > L. > > On Wed, 2008-11-05 at 18:21 -0500, Mathe, Ewy (NIH/NCI) [F] wrote: >> Hello, >> >> >> >> My goal is to preprocess and normalize Affy Mouse Gene 1.0 ST >> arrays but am having difficulty doing so in R. >> >> >> >> I have successfully built my own annotation package, which has the >> name "pd.mogene.1.0.st.v1". However, after loading the package and >> reading in my CEL files, it does not automatically annotate the >> dataset and outputs the following: >> >> >> >>> data >> AffyBatch object >> size of arrays=1050x1050 features (14 kb) >> cdf=pd.mogene.1.0.st.v1 (??? affyids) >> number of samples=8 >> Error in getCdfInfo(object) : >> Could not obtain CDF environment, problems encountered: >> Specified environment does not contain pd.mogene.1.0.st.v1 >> Library - package pd.mogene.1.0.st.v1cdf not installed >> Data for package affy did not contain pd.mogene.1.0.st.v1cdf >> Bioconductor - could not connect >> In addition: Warning messages: >> 1: In readLines(biocURL) : >> cannot open: HTTP status was '503 Service Unavailable' >> 2: missing cdf environment! in show(AffyBatch) >> 3: In readLines(biocURL) : >> cannot open: HTTP status was '503 Service Unavailable' >> >> >> >> >> >> For some reason, the package names are not synchronized but I >> cannot figure out how to rebuild the package by specifying the >> name. This is the code I used to build the package: >> >> >> >> pgfFile <- "MoGene-1_0-st-v1.r3.pgf" >> >> clfFile <- "MoGene-1_0-st-v1.r3.clf" >> >> transFile <- "MoGene-1_0-st-v1.na26.mm9.transcript.csv" >> >> probeFile <- "MoGene-1_0-st-v1.probe.tab" >> >> pkg <- new("AffyGenePDInfoPkgSeed", author = "em", email = >> >> "mathee at mail.nih.gov", version = "0.0.1", genomebuild = >> "thegenomebuilddate", >> >> biocViews = "AnnotationData", pgfFile = pgfFile, clfFile = clfFile, >> >> transFile = transFile, probeFile = probeFile) >> >> makePdInfoPackage(pkg,destDir=".") >> >> >> >> Thanks in advance for any input you can give me on this! >> >> >> >> Ewy >> >> >> >> Ewy Math, Ph. D. >> >> Laboratory of Human Carcinogenesis >> >> National Cancer Institute, NIH >> >> 37 Convent Drive >> >> Building 37, Room 3068 >> >> Bethesda, MD 20892-4255 >> >> Tel: 301-496-5835 >> >> Fax: 301-496-0497 >> >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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 ------------------------------ Mark Robinson Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robinson at garvan.org.au e: mrobinson at wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852

Hello everyone, Switching to the oligo package did the trick! Many thanks, Ewy -----Original Message----- From: Mathe, Ewy (NIH/NCI) [F] Sent: Thursday, November 06, 2008 7:50 AM To: Mark Robinson; laurent Cc: bioconductor at stat.math.ethz.ch Subject: RE: [BioC] CDF issue Mark, Laurent, and Benilton, Thank you all for your comments, I will give your suggestions a try and let you know. Best, Ewy -----Original Message----- From: Mark Robinson [mailto:mrobinson@wehi.EDU.AU] Sent: Thu 11/6/2008 7:07 AM To: laurent Cc: Mathe, Ewy (NIH/NCI) [F]; bioconductor at stat.math.ethz.ch Subject: Re: [BioC] CDF issue Hi Ewy. Just to follow up on Laurent's post. I'm afraid I can't speak to the problems you are having below ... but I do know of at least 3 ways to preprocess Gene 1.0 ST data (say, with RMA) in R: 1. aroma.affymetrix http://groups.google.com/group/aroma-affymetrix/web/mogene-1-0-st-v1 (can follow mostly the same steps as in http://groups.google.com/group/aroma-affymetrix/web/human-exon-array- ana lysis) 2. xps package https://stat.ethz.ch/pipermail/bioconductor/2008-May/022267.html 3. as you were doing, perhaps spelled out a little better at (+ using 'rma' in the oligo package): http://article.gmane.org/gmane.science.biology.informatics.conductor/1 89 63/ HTH, Mark On 06/11/2008, at 5:24 PM, laurent wrote: > Hi Mathe, > > For historical reasons, the "annotation" is the association between > probe sets and gene name, chromosomal location, etc... > The CDF data structure models the files with extension .cdf (Chip > Definition File), and contains the association between probe position > on the array and the probe set the probe belongs to. > > This earlier post is related to the problem you are having: > https://stat.ethz.ch/pipermail/bioconductor/2007-November/020188.html > > > > L. > > On Wed, 2008-11-05 at 18:21 -0500, Mathe, Ewy (NIH/NCI) [F] wrote: >> Hello, >> >> >> >> My goal is to preprocess and normalize Affy Mouse Gene 1.0 ST >> arrays but am having difficulty doing so in R. >> >> >> >> I have successfully built my own annotation package, which has the >> name "pd.mogene.1.0.st.v1". However, after loading the package and >> reading in my CEL files, it does not automatically annotate the >> dataset and outputs the following: >> >> >> >>> data >> AffyBatch object >> size of arrays=1050x1050 features (14 kb) >> cdf=pd.mogene.1.0.st.v1 (??? affyids) >> number of samples=8 >> Error in getCdfInfo(object) : >> Could not obtain CDF environment, problems encountered: >> Specified environment does not contain pd.mogene.1.0.st.v1 >> Library - package pd.mogene.1.0.st.v1cdf not installed >> Data for package affy did not contain pd.mogene.1.0.st.v1cdf >> Bioconductor - could not connect >> In addition: Warning messages: >> 1: In readLines(biocURL) : >> cannot open: HTTP status was '503 Service Unavailable' >> 2: missing cdf environment! in show(AffyBatch) >> 3: In readLines(biocURL) : >> cannot open: HTTP status was '503 Service Unavailable' >> >> >> >> >> >> For some reason, the package names are not synchronized but I >> cannot figure out how to rebuild the package by specifying the >> name. This is the code I used to build the package: >> >> >> >> pgfFile <- "MoGene-1_0-st-v1.r3.pgf" >> >> clfFile <- "MoGene-1_0-st-v1.r3.clf" >> >> transFile <- "MoGene-1_0-st-v1.na26.mm9.transcript.csv" >> >> probeFile <- "MoGene-1_0-st-v1.probe.tab" >> >> pkg <- new("AffyGenePDInfoPkgSeed", author = "em", email = >> >> "mathee at mail.nih.gov", version = "0.0.1", genomebuild = >> "thegenomebuilddate", >> >> biocViews = "AnnotationData", pgfFile = pgfFile, clfFile = clfFile, >> >> transFile = transFile, probeFile = probeFile) >> >> makePdInfoPackage(pkg,destDir=".") >> >> >> >> Thanks in advance for any input you can give me on this! >> >> >> >> Ewy >> >> >> >> Ewy Math, Ph. D. >> >> Laboratory of Human Carcinogenesis >> >> National Cancer Institute, NIH >> >> 37 Convent Drive >> >> Building 37, Room 3068 >> >> Bethesda, MD 20892-4255 >> >> Tel: 301-496-5835 >> >> Fax: 301-496-0497 >> >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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 ------------------------------ Mark Robinson Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robinson at garvan.org.au e: mrobinson at wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852