Hi all, I've been trying to process a set of Affy MoGene-1_0-st-v1 CEL files with the "oligo" package. Using the "pd.mogene.1.0.st.v1" library, I can quite easily do read.celfiles followed by rma. But this library is built at the probeset level. Does anyone have recommendations of how to end up working at the transcript level? I thought I could simply build a new PdInfoPackage, using the transcript mapping file from Affy instead of the probeset, but that didn't seem to work (code below). Many thanks, Cei library(AffyCompatible) library(pdInfoBuilder) seed <- new("AffyGenePDInfoPkgSeed", pgfFile = "MoGene-1_0-st-v1.r4.pgf", clfFile = "MoGene-1_0-st-v1.r4.clf", probeFile = "MoGene-1_0-st-v1.na28.mm9.transcript.csv", author = "Cei Abreu-Goodger", email = "cei at ebi.ac.uk", biocViews = "AnnotationData", genomebuild = "mm9", organism = "Mus musculus", species = "Mouse") makePdInfoPackage(seed, destDir=".") ====================================================================== ========== Building annotation package for Affymetrix Gene ST Array PGF.....: MoGene-1_0-st-v1.r4.pgf CLF.....: MoGene-1_0-st-v1.r4.clf Probeset: MoGene-1_0-st-v1.na28.mm9.transcript.csv ====================================================================== ========== Parsing file: MoGene-1_0-st-v1.r4.pgf ... OK Parsing file: MoGene-1_0-st-v1.r4.clf ... OK Creating initial table for probes...OK Creating dictionaries... OK Parsing file: MoGene-1_0-st-v1.na28.mm9.transcript.csv ... OK Error in `[.data.frame`(probesets, , cols) : undefined columns selected In addition: Warning messages: > sessionInfo() R version 2.9.0 (2009-04-17) i386-apple-darwin8.11.1 locale: en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] grid stats graphics grDevices datasets utils methods [8] base other attached packages: [1] gplots_2.7.1 caTools_1.9 [3] bitops_1.0-4.1 gdata_2.4.2 [5] gtools_2.6.1 oligo_1.8.1 [7] preprocessCore_1.6.0 pd.mogene.1.0.st.v1_0.0.1 [9] oligoClasses_1.6.0 RSQLite_0.7-1 [11] DBI_0.2-4 Biobase_2.4.1 loaded via a namespace (and not attached): [1] affxparser_1.16.0 affyio_1.12.0 Biostrings_2.12.5 IRanges_1.2.2 [5] splines_2.9.0

Dear Cei I am not sure if I can help you, but for the transcript level you need to start with "MoGene-1_0-st-v1.r3.pgf", which groups the probes at the transcript level, whereas "MoGene-1_0-st-v1.r4.pgf" groups the probes at the probeset level (as for the exon arrays). There exist two libraries "mogene10sttranscriptcluster.db" and "mogene10stprobeset.db" which can be downloaded from BioC. Alternatively, you could use package "xps" which supports both the transcript level and the probeset level. Best regards Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._ Cei Abreu-Goodger wrote: > Hi all, > > I've been trying to process a set of Affy MoGene-1_0-st-v1 CEL files > with the "oligo" package. Using the "pd.mogene.1.0.st.v1" library, I > can quite easily do read.celfiles followed by rma. But this library is > built at the probeset level. > > Does anyone have recommendations of how to end up working at the > transcript level? > > I thought I could simply build a new PdInfoPackage, using the > transcript mapping file from Affy instead of the probeset, but that > didn't seem to work (code below). > > Many thanks, > > Cei > > > library(AffyCompatible) > library(pdInfoBuilder) > > seed <- new("AffyGenePDInfoPkgSeed", > pgfFile = "MoGene-1_0-st-v1.r4.pgf", clfFile = > "MoGene-1_0-st-v1.r4.clf", > probeFile = "MoGene-1_0-st-v1.na28.mm9.transcript.csv", > author = "Cei Abreu-Goodger", > email = "cei at ebi.ac.uk", biocViews = "AnnotationData", > genomebuild = "mm9", > organism = "Mus musculus", species = "Mouse") > > makePdInfoPackage(seed, destDir=".") > > > ==================================================================== ============ > > Building annotation package for Affymetrix Gene ST Array > PGF.....: MoGene-1_0-st-v1.r4.pgf > CLF.....: MoGene-1_0-st-v1.r4.clf > Probeset: MoGene-1_0-st-v1.na28.mm9.transcript.csv > ==================================================================== ============ > > Parsing file: MoGene-1_0-st-v1.r4.pgf ... OK > Parsing file: MoGene-1_0-st-v1.r4.clf ... OK > Creating initial table for probes...OK > Creating dictionaries... OK > Parsing file: MoGene-1_0-st-v1.na28.mm9.transcript.csv ... OK > Error in `[.data.frame`(probesets, , cols) : undefined columns selected > In addition: Warning messages: > > > > sessionInfo() > R version 2.9.0 (2009-04-17) > i386-apple-darwin8.11.1 > > locale: > en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] grid stats graphics grDevices datasets utils methods > [8] base > > other attached packages: > [1] gplots_2.7.1 caTools_1.9 > [3] bitops_1.0-4.1 gdata_2.4.2 > [5] gtools_2.6.1 oligo_1.8.1 > [7] preprocessCore_1.6.0 pd.mogene.1.0.st.v1_0.0.1 > [9] oligoClasses_1.6.0 RSQLite_0.7-1 > [11] DBI_0.2-4 Biobase_2.4.1 > > loaded via a namespace (and not attached): > [1] affxparser_1.16.0 affyio_1.12.0 Biostrings_2.12.5 IRanges_1.2.2 > [5] splines_2.9.0 > > _______________________________________________ > 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 > >