CDF issue
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@mathe-ewy-nihnci-f-3124
Last seen 9.6 years ago
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@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 Mathé, 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]]
Annotation Cancer cdf annotate affy Annotation Cancer cdf annotate affy • 1.4k views
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laurent ▴ 140
@laurent-3110
Last seen 9.1 years ago
United States
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
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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
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@mathe-ewy-nihnci-f-3124
Last seen 9.6 years ago
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-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
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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
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