eset -Affy Mouse Gene 1.0 ST. Array-
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@alessandro-brozzi-5276
Last seen 9.9 years ago
European Union
hi all, I'm working on Affy Mouse Gene 1.0 ST. Array. If I do: rawData = ReadAffy() eset = rma(rawData) I end up with 34760 Features which correspond to transcript_cluster_id. Each transcript_cluster_id is formed by several probe_ids How can I make an eset with the probe_id levels not summarized in transcript_cluster s? thanks in advance, Alex * ----------------------------- Alessandro Brozzi, PhD Department of Mathematics University of Perugia, Via Vanvitelli 1, 06123 Perugia, Italy tel: + 39 075 585 5039 fax: **+ 39 075 585 5024 * [[alternative HTML version deleted]]
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@james-w-macdonald-5106
Last seen 19 hours ago
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Hi Alessandro, On 5/10/2012 6:39 AM, alessandro brozzi wrote: > hi all, > I'm working on Affy Mouse Gene 1.0 ST. Array. > > If I do: > > rawData = ReadAffy() > eset = rma(rawData) > > I end up with 34760 Features which correspond to transcript_cluster_id. > Each transcript_cluster_id is formed by several probe_ids > > How can I make an eset with the probe_id levels not summarized in > transcript_cluster > s? Don't use the affy package. library(oligo) rawData <- read.celfiles(list.celfiles()) eset <- rma(rawData, target = "probeset") This will summarize at the probeset level, which is roughly the exon level (some probesets span multiple exons). Best, Jim > > thanks in advance, > Alex > * > ----------------------------- > Alessandro Brozzi, PhD > Department of Mathematics > University of Perugia, > Via Vanvitelli 1, 06123 Perugia, Italy > tel: + 39 075 585 5039 > fax: **+ 39 075 585 5024 > * > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Dear List, I have a set of the new AraGene 1.1-st arrays and thus like to build a corresponding pdInfo package. Anyway, I get an error while creating the package. Please see code and error mesasge below. Obviously, the mps file for the array can't be found, and I was unable to figure out how to specify the file location in the new("AffyGenePDInfoPkgSeed", ... ) function. Looking through the vignette, archive and help files I never came across the mps message, so any suggestion on how to specify the file (which is also in the working directory). Thank you very much in advance, Michael baseDir = "F:/Auswertung/Array Annotationen/Affy" > (pgf <- list.files(paste(baseDir, "MO_AraGene-1_1-st-v1_strip_libraryfile", sep="/"), pattern = ".pgf", full.names = TRUE)) [1] "F:/Auswertung/Array Annotationen/Affy/MO_AraGene-1_1-st-v1_strip_libraryfile/AraGene- 1_1-st.pgf" > (clf <- list.files(paste(baseDir, "MO_AraGene-1_1-st-v1_strip_libraryfile", sep="/"), pattern = ".clf", full.names = TRUE)) [1] "F:/Auswertung/Array Annotationen/Affy/MO_AraGene-1_1-st-v1_strip_libraryfile/AraGene- 1_1-st.clf" > (prob <- list.files(baseDir, pattern = "tair10.probeset.csv",full.names = TRUE)) [1] "F:/Auswertung/Array Annotationen/Affy/AraGene-1_1-st-v1.na32.tair10.probeset.csv" > (trans = list.files(baseDir, pattern = "tair10.transcript.csv",full.names = TRUE)) [1] "F:/Auswertung/Array Annotationen/Affy/AraGene-1_1-st-v1.na32.tair10.transcript.csv" > (core = list.files(paste(baseDir, "MO_AraGene-1_1-st-v1_strip_libraryfile", sep="/"), pattern = ".mps", full.names = TRUE)) [1] "F:/Auswertung/Array Annotationen/Affy/MO_AraGene-1_1-st-v1_strip_libraryfile/AraGene- 1_1-st.mps" > > seed <- new("AffyGenePDInfoPkgSeed", + pgfFile = pgf, clfFile = clf, + probeFile = prob, author = "Michael Walter", + transFile = trans, + email = "michael.walter at med.uni-tuebingen.de", + biocViews = "AnnotationData", + genomebuild = "TAIR10", + organism = "Arabidopsis", species = "Arabidopsis thaliana") > > makePdInfoPackage(seed, destDir = ".") =================================================================== ========= ==== Building annotation package for Affymetrix Gene ST Array PGF.........: AraGene-1_1-st.pgf CLF.........: AraGene-1_1-st.clf Probeset....: AraGene-1_1-st-v1.na32.tair10.probeset.csv Transcript..: AraGene-1_1-st-v1.na32.tair10.transcript.csv Core MPS....: coreMps =================================================================== ========= ==== Parsing file: AraGene-1_1-st.pgf... OK Parsing file: AraGene-1_1-st.clf... OK Creating initial table for probes... OK Creating dictionaries... OK Parsing file: AraGene-1_1-st-v1.na32.tair10.probeset.csv... OK Parsing file: coreMps... Fehler in file(file, "rt") : kann Verbindung nicht ?ffnen Zus?tzlich: Warnmeldungen: 1: In is.na(x) : is.na() auf nicht-(Liste oder Vektor) des Typs 'NULL' angewendet 2: In is.na(x) : is.na() auf nicht-(Liste oder Vektor) des Typs 'NULL' angewendet 3: In file(file, "rt") : kann Datei 'coreMps' nicht ?ffnen: No such file or directory > > sessionInfo() R version 2.14.0 (2011-10-31) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C [5] LC_TIME=German_Germany.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pdInfoBuilder_1.20.0 affxparser_1.26.4 RSQLite_0.11.1 [4] DBI_0.2-5 oligo_1.18.1 oligoClasses_1.16.0 [7] Biobase_2.14.0 loaded via a namespace (and not attached): [1] affyio_1.22.0 Biostrings_2.22.0 bit_1.1-8 [4] ff_2.2-6 IRanges_1.12.6 preprocessCore_1.16.0 [7] splines_2.14.0 tools_2.14.0 zlibbioc_1.0.1 > -- Dr. Michael Walter MFT Services University of T?bingen Calwerstr. 7 72076 T?bingen Tel.: +49 7071 29 83210 Fax. + 49 7071 29 5228 web: www.mft-services.de Confidentiality Note: This message is intended only for the use of the named recipient(s) and may contain confidential and/or proprietary information. If you are not the inte nded recipient, please contact the sender and delete the message. Any unauthorize d use of the information contained in this message is prohibited.
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If you update to R-2.15.0 (the current one), you can install the annotation package with: biocLite('pd.aragene.1.1.st') http://www.bioconductor.org/packages/2.10/data/annotation/html/pd.arag ene.1.1.st.html best, b On 10 May 2012 14:41, Mike Walter <michael_walter at="" email.de=""> wrote: > > ? Dear List, > ? I have a set of the new AraGene 1.1-st arrays and thus like to build a > ? corresponding pdInfo package. Anyway, I get an error while creating the > ? package. Please see code and error mesasge below. Obviously, the mps file > ? for the array can't be found, and I was unable to figure out how to specify > ? the ?file location in the new("AffyGenePDInfoPkgSeed", ... ) function. > ? Looking through the vignette, archive and help files I never came across the > ? mps message, so any suggestion on how to specify the file (which is also in > ? the working directory). > ? Thank you very much in advance, > ? Michael > ? baseDir = "F:/Auswertung/Array Annotationen/Affy" > ? > (pgf <- list.files(paste(baseDir, > ? "MO_AraGene-1_1-st-v1_strip_libraryfile", ?sep="/"), pattern = ".pgf", > ? full.names = TRUE)) > ? [1] "F:/Auswertung/Array > ? Annotationen/Affy/MO_AraGene-1_1-st-v1_strip_libraryfile/AraGene- 1_1-st.pgf" > ? > (clf <- list.files(paste(baseDir, > ? "MO_AraGene-1_1-st-v1_strip_libraryfile", ?sep="/"), pattern = ".clf", > ? full.names = TRUE)) > ? [1] "F:/Auswertung/Array > ? Annotationen/Affy/MO_AraGene-1_1-st-v1_strip_libraryfile/AraGene- 1_1-st.clf" > ? > (prob <- list.files(baseDir, pattern = "tair10.probeset.csv",full.names = > ? TRUE)) > ? [1] "F:/Auswertung/Array > ? Annotationen/Affy/AraGene-1_1-st-v1.na32.tair10.probeset.csv" > ? > (trans = list.files(baseDir, pattern = "tair10.transcript.csv",full.names > ? = TRUE)) > ? [1] "F:/Auswertung/Array > ? Annotationen/Affy/AraGene-1_1-st-v1.na32.tair10.transcript.csv" > ? > (core = list.files(paste(baseDir, > ? "MO_AraGene-1_1-st-v1_strip_libraryfile", ?sep="/"), pattern = ".mps", > ? full.names = TRUE)) > ? [1] "F:/Auswertung/Array > ? Annotationen/Affy/MO_AraGene-1_1-st-v1_strip_libraryfile/AraGene- 1_1-st.mps" > ? > > ? > seed <- new("AffyGenePDInfoPkgSeed", > ? + pgfFile = pgf, clfFile = clf, > ? + probeFile = prob, author = "Michael Walter", > ? + transFile = trans, > ? + email = "michael.walter at med.uni-tuebingen.de", > ? + biocViews = "AnnotationData", > ? + genomebuild = "TAIR10", > ? + organism = "Arabidopsis", species = "Arabidopsis thaliana") > ? > > ? > makePdInfoPackage(seed, destDir = ".") > ? ================================================================== ========== > ? ==== > ? Building annotation package for Affymetrix Gene ST Array > ? PGF.........: AraGene-1_1-st.pgf > ? CLF.........: AraGene-1_1-st.clf > ? Probeset....: AraGene-1_1-st-v1.na32.tair10.probeset.csv > ? Transcript..: AraGene-1_1-st-v1.na32.tair10.transcript.csv > ? Core MPS....: coreMps > ? ================================================================== ========== > ? ==== > ? Parsing file: AraGene-1_1-st.pgf... OK > ? Parsing file: AraGene-1_1-st.clf... OK > ? Creating initial table for probes... OK > ? Creating dictionaries... OK > ? Parsing file: AraGene-1_1-st-v1.na32.tair10.probeset.csv... OK > ? Parsing file: coreMps... Fehler in file(file, "rt") : kann Verbindung nicht > ? ?ffnen > ? Zus?tzlich: Warnmeldungen: > ? 1: In is.na(x) : > ? ? is.na() auf nicht-(Liste oder Vektor) des Typs 'NULL' angewendet > ? 2: In is.na(x) : > ? ? is.na() auf nicht-(Liste oder Vektor) des Typs 'NULL' angewendet > ? 3: In file(file, "rt") : > ? ? kann Datei 'coreMps' nicht ?ffnen: No such file or directory > ? > > ? > sessionInfo() > ? R version 2.14.0 (2011-10-31) > ? Platform: i386-pc-mingw32/i386 (32-bit) > ? locale: > ? [1] LC_COLLATE=German_Germany.1252 ?LC_CTYPE=German_Germany.1252 > ? [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C > ? [5] LC_TIME=German_Germany.1252 > ? attached base packages: > ? [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > ? other attached packages: > ? [1] pdInfoBuilder_1.20.0 affxparser_1.26.4 ? ?RSQLite_0.11.1 > ? [4] DBI_0.2-5 ? ? ? ? ? ?oligo_1.18.1 ? ? ? ? oligoClasses_1.16.0 > ? [7] Biobase_2.14.0 > ? loaded via a namespace (and not attached): > ? [1] affyio_1.22.0 ? ? ? ? Biostrings_2.22.0 ? ? bit_1.1-8 > ? [4] ff_2.2-6 ? ? ? ? ? ? ?IRanges_1.12.6 ? ? ? ?preprocessCore_1.16.0 > ? [7] splines_2.14.0 ? ? ? ?tools_2.14.0 ? ? ? ? ?zlibbioc_1.0.1 > ? > > ? -- > ? Dr. Michael Walter > ? MFT Services > ? University of T?bingen > ? Calwerstr. 7 > ? 72076 ?T?bingen > ? Tel.: +49 7071 29 83210 > ? Fax. + 49 7071 29 5228 > ? web: www.mft-services.de > ? Confidentiality Note: > ? This message is intended only for the use of the named recipient(s) and may > ? contain confidential and/or proprietary information. If you are not the inte > ? nded > ? recipient, please contact the sender and delete the message. Any unauthorize > ? d > ? use of the information contained in this message is prohibited. > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi Benilton, Thank you very much. I'll go and update my R Version. Kind regards, Michael -- Dr. Michael Walter MFT Services University of T?bingen Calwerstr. 7 72076 T?bingen Tel.: +49 7071 29 83210 Fax. + 49 7071 29 5228 web: www.mft-services.de Confidentiality Note: This message is intended only for the use of the named recipient(s) and may contain confidential and/or proprietary information. If you are not the inte nded recipient, please contact the sender and delete the message. Any unauthorize d use of the information contained in this message is prohibited. Gesendet: Donnerstag, 10. Mai 2012 um 16:38 Uhr Von: "Benilton Carvalho" <beniltoncarvalho at="" gmail.com=""> An: "Mike Walter" <michael_walter at="" email.de=""> Cc: bioconductor at r-project.org Betreff: Re: [BioC] pdInfoBuilder: coreMps If you update to R-2.15.0 (the current one), you can install the annotation package with: biocLite('pd.aragene.1.1.st') [1]http://www.bioconductor.org/packages/2.10/data/annotation/html/p d.aragene .1.1.st.html best, b On 10 May 2012 14:41, Mike Walter <michael_walter at="" email.de=""> wrote: > > Dear List, > I have a set of the new AraGene 1.1-st arrays and thus like to build a > corresponding pdInfo package. Anyway, I get an error while creating the > package. Please see code and error mesasge below. Obviously, the mps file > for the array can't be found, and I was unable to figure out how to specify > the file location in the new("AffyGenePDInfoPkgSeed", ... ) function. > Looking through the vignette, archive and help files I never came across the > mps message, so any suggestion on how to specify the file (which is also in > the working directory). > Thank you very much in advance, > Michael > baseDir = "F:/Auswertung/Array Annotationen/Affy" > > (pgf <- list.files(paste(baseDir, > "MO_AraGene-1_1-st-v1_strip_libraryfile", sep="/"), pattern = ".pgf", > full.names = TRUE)) > [1] "F:/Auswertung/Array > Annotationen/Affy/MO_AraGene-1_1-st-v1_strip_libraryfile/AraGene- 1_1-st.pgf" > > (clf <- list.files(paste(baseDir, > "MO_AraGene-1_1-st-v1_strip_libraryfile", sep="/"), pattern = ".clf", > full.names = TRUE)) > [1] "F:/Auswertung/Array > Annotationen/Affy/MO_AraGene-1_1-st-v1_strip_libraryfile/AraGene- 1_1-st.clf" > > (prob <- list.files(baseDir, pattern = "tair10.probeset.csv",full.names = > TRUE)) > [1] "F:/Auswertung/Array > Annotationen/Affy/AraGene-1_1-st-v1.na32.tair10.probeset.csv" > > (trans = list.files(baseDir, pattern = "tair10.transcript.csv",full.names > = TRUE)) > [1] "F:/Auswertung/Array > Annotationen/Affy/AraGene-1_1-st-v1.na32.tair10.transcript.csv" > > (core = list.files(paste(baseDir, > "MO_AraGene-1_1-st-v1_strip_libraryfile", sep="/"), pattern = ".mps", > full.names = TRUE)) > [1] "F:/Auswertung/Array > Annotationen/Affy/MO_AraGene-1_1-st-v1_strip_libraryfile/AraGene- 1_1-st.mps" > > > > seed <- new("AffyGenePDInfoPkgSeed", > + pgfFile = pgf, clfFile = clf, > + probeFile = prob, author = "Michael Walter", > + transFile = trans, > + email = "michael.walter at med.uni-tuebingen.de", > + biocViews = "AnnotationData", > + genomebuild = "TAIR10", > + organism = "Arabidopsis", species = "Arabidopsis thaliana") > > > > makePdInfoPackage(seed, destDir = ".") > =================================================================== ========= > ==== > Building annotation package for Affymetrix Gene ST Array > PGF.........: AraGene-1_1-st.pgf > CLF.........: AraGene-1_1-st.clf > Probeset....: AraGene-1_1-st-v1.na32.tair10.probeset.csv > Transcript..: AraGene-1_1-st-v1.na32.tair10.transcript.csv > Core MPS....: coreMps > =================================================================== ========= > ==== > Parsing file: AraGene-1_1-st.pgf... OK > Parsing file: AraGene-1_1-st.clf... OK > Creating initial table for probes... OK > Creating dictionaries... OK > Parsing file: AraGene-1_1-st-v1.na32.tair10.probeset.csv... OK > Parsing file: coreMps... Fehler in file(file, "rt") : kann Verbindung nicht > ?ffnen > Zus?tzlich: Warnmeldungen: > 1: In is.na(x) : > is.na() auf nicht-(Liste oder Vektor) des Typs 'NULL' angewendet > 2: In is.na(x) : > is.na() auf nicht-(Liste oder Vektor) des Typs 'NULL' angewendet > 3: In file(file, "rt") : > kann Datei 'coreMps' nicht ?ffnen: No such file or directory > > > > sessionInfo() > R version 2.14.0 (2011-10-31) > Platform: i386-pc-mingw32/i386 (32-bit) > locale: > [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 > [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C > [5] LC_TIME=German_Germany.1252 > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] pdInfoBuilder_1.20.0 affxparser_1.26.4 RSQLite_0.11.1 > [4] DBI_0.2-5 oligo_1.18.1 oligoClasses_1.16.0 > [7] Biobase_2.14.0 > loaded via a namespace (and not attached): > [1] affyio_1.22.0 Biostrings_2.22.0 bit_1.1-8 > [4] ff_2.2-6 IRanges_1.12.6 preprocessCore_1.16.0 > [7] splines_2.14.0 tools_2.14.0 zlibbioc_1.0.1 > > > -- > Dr. Michael Walter > MFT Services > University of T?bingen > Calwerstr. 7 > 72076 T?bingen > Tel.: +49 7071 29 83210 > Fax. + 49 7071 29 5228 > web: [2]www.mft-services.de > Confidentiality Note: > This message is intended only for the use of the named recipient(s) and may > contain confidential and/or proprietary information. If you are not the inte > nded > recipient, please contact the sender and delete the message. Any unauthorize > d > use of the information contained in this message is prohibited. > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > [3]https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: [4]http://news.gmane.org/gmane.science.biology.informatics.conductor References 1. http://www.bioconductor.org/packages/2.10/data/annotation/html/p d.aragene.1.1.st.html 2. http://www.mft-services.de/ 3. https://stat.ethz.ch/mailman/listinfo/bioconductor 4. http://news.gmane.org/gmane.science.biology.informatics.conductor
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@alessandro-brozzi-5276
Last seen 9.9 years ago
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hi all, I'm working on Affy Mouse Gene 1.0 ST. Array. If I do: rawData = ReadAffy() eset = rma(rawData) I end up with 34760 Features which correspond to transcript_cluster_id. Each transcript_cluster_id is formed by several probe_ids How can I make an eset with the probe_id levels not summarized in transcript_cluster s? thanks in advance, Alex * ----------------------------- Alessandro Brozzi, PhD Department of Mathematics University of Perugia, Via Vanvitelli 1, 06123 Perugia, Italy tel: + 39 075 585 5039 fax: **+ 39 075 585 5024 * [[alternative HTML version deleted]]
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Hi Alex, try to use the alternative CDFs from Brainarray. They provide a better probe mapping which is based on the latest genome and transcriptome information. Install the aCDFs of interest, change rawData at cdfName to the corresponding aCDF, afterwards run the summarization and that's all. Cheers, Okko -- dipl.-inf. djork clevert | gleimstr. 13a | d-10437 berlin e: okko at clevert.de p: +49.30.4432 4702 f: +49.30.6883 5307 Am 10.05.2012 um 12:43 schrieb alessandro brozzi: > hi all, > I'm working on Affy Mouse Gene 1.0 ST. Array. > > If I do: > > rawData = ReadAffy() > eset = rma(rawData) > > I end up with 34760 Features which correspond to transcript_cluster_id. > Each transcript_cluster_id is formed by several probe_ids > > How can I make an eset with the probe_id levels not summarized in > transcript_cluster > s? > > thanks in advance, > Alex > * > ----------------------------- > Alessandro Brozzi, PhD > Department of Mathematics > University of Perugia, > Via Vanvitelli 1, 06123 Perugia, Italy > tel: + 39 075 585 5039 > fax: **+ 39 075 585 5024 > * > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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