Hi, I am trying to feed the mouse Gene 1.0 ST array into our R pipeline (affy -> gcrma->limma). At the first I got an error during the gcrma step: Adjusting for optical effect....Done. Computing affinities[1] "Checking to see if your internet connection works..." [1] "Environment mogene10stv1probe was not found in the Bioconductor repository." Error in get(probepackagename) : object 'mogene10stv1probe' not found I then download the mogene10stv1probe from bioconductor 2.8 and installed the package manually & rerun the pipeline: now i am getting a new error: > dd = gcrma(abatch) Adjusting for optical effect....Done. Computing affinitiesLoading required package: AnnotationDbi Error: length(prlen) == 1 is not TRUE I google on the error and it seem there is some problem with the probe length (instead of 25bp, some probe are 21 bp) probepkgname ="mogene10stv1probe" > seq = get(probepkgname) > prlen=nchar(seq$seq) > range(prlen) [1] 21 25 Any idea, advice would be appreciated! ( I copied the sample code & session infor at the end of email) Thanks a lot! Yupu R version 2.10.0 (2009-10-26) Copyright (C) 2009 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(gcrma) Loading required package: affy Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. > library(affy) > cel.dir.zip = "/ifs/e63data/galaxy/galaxy- dist/database/files/000/dataset_396_files/rexpression.cel.zip" > cel.dir = dirname(cel.dir.zip) > abatch = ReadAffy(celfile.path=cel.dir) > dd = gcrma(abatch) Adjusting for optical effect....Done. Computing affinitiesLoading required package: AnnotationDbi Error: length(prlen) == 1 is not TRUE > probepkgname ="mogene10stv1probe" > seq = get(probepkgname) > prlen=nchar(seq$seq) > range(prlen) [1] 21 25 > sessionInfo() R version 2.10.0 (2009-10-26) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] mogene10stv1probe_2.8.0 AnnotationDbi_1.14.1 mogene10stv1cdf_2.8.0 [4] gcrma_2.18.1 affy_1.24.2 Biobase_2.6.1 loaded via a namespace (and not attached): [1] affyio_1.14.0 Biostrings_2.14.12 DBI_0.2-5 [4] IRanges_1.4.16 preprocessCore_1.8.0 RSQLite_0.9-4 [7] splines_2.10.0 tools_2.10.0

Hi Yupu, First: update to the latest version of R/BioC; the one you are using is quite old. You may want to have a look at the suggestion Mike Smith proposed few months ago: http://article.gmane.org/gmane.science.biology.informatics.conductor/3 2506 Note: I didn't try it myself, so I cannot comment any further on it. HTH, Guido --------------------------------------------------------- Guido Hooiveld, PhD Nutrition, Metabolism & Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 email: guido.hooiveld at wur.nl internet: http://nutrigene.4t.com http://www.researcherid.com/rid/F-4912-2010 -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project.org] On Behalf Of Yupu Liang Sent: Thursday, September 29, 2011 17:59 To: bioconductor at r-project.org Subject: [BioC] gcrma failed on mouse Gene 1.0 ST array Hi, I am trying to feed the mouse Gene 1.0 ST array into our R pipeline (affy -> gcrma->limma). At the first I got an error during the gcrma step: Adjusting for optical effect....Done. Computing affinities[1] "Checking to see if your internet connection works..." [1] "Environment mogene10stv1probe was not found in the Bioconductor repository." Error in get(probepackagename) : object 'mogene10stv1probe' not found I then download the mogene10stv1probe from bioconductor 2.8 and installed the package manually & rerun the pipeline: now i am getting a new error: > dd = gcrma(abatch) Adjusting for optical effect....Done. Computing affinitiesLoading required package: AnnotationDbi Error: length(prlen) == 1 is not TRUE I google on the error and it seem there is some problem with the probe length (instead of 25bp, some probe are 21 bp) probepkgname ="mogene10stv1probe" > seq = get(probepkgname) > prlen=nchar(seq$seq) > range(prlen) [1] 21 25 Any idea, advice would be appreciated! ( I copied the sample code & session infor at the end of email) Thanks a lot! Yupu R version 2.10.0 (2009-10-26) Copyright (C) 2009 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(gcrma) Loading required package: affy Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. > library(affy) > cel.dir.zip = "/ifs/e63data/galaxy/galaxy- dist/database/files/000/dataset_396_files/rexpression.cel.zip" > cel.dir = dirname(cel.dir.zip) > abatch = ReadAffy(celfile.path=cel.dir) dd = gcrma(abatch) Adjusting for optical effect....Done. Computing affinitiesLoading required package: AnnotationDbi Error: length(prlen) == 1 is not TRUE > probepkgname ="mogene10stv1probe" > seq = get(probepkgname) > prlen=nchar(seq$seq) > range(prlen) [1] 21 25 > sessionInfo() R version 2.10.0 (2009-10-26) x86_64-unknown-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] mogene10stv1probe_2.8.0 AnnotationDbi_1.14.1 mogene10stv1cdf_2.8.0 [4] gcrma_2.18.1 affy_1.24.2 Biobase_2.6.1 loaded via a namespace (and not attached): [1] affyio_1.14.0 Biostrings_2.14.12 DBI_0.2-5 [4] IRanges_1.4.16 preprocessCore_1.8.0 RSQLite_0.9-4 [7] splines_2.10.0 tools_2.10.0 _______________________________________________ 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