Hi, I am having a problem running the following code which utilizes an eset derived from hthgu133a CEL files. >eset ExpressionSet (storageMode: lockedEnvironment) assayData: 13834 features, 9 samples element names: exprs, se.exprs phenoData sampleNames: <<masked>> (9 total) varLabels and varMetadata description: sample: arbitrary numbering CEL: NA phenotype: NA ShortName: NA featureData featureNames: 1007_s_at, 1053_at, ..., AFFX-r2-Ec-bioD-5_at (13834 total) fvarLabels and fvarMetadata description: none experimentData: use 'experimentData(object)' Annotation: hthgu133a >library(genefilter) >nsF = nsFilter(eset, var.filter = FALSE)$eset Error in .checkKeys(value, Lkeys(x), x at ifnotfound) : value for "AFFX-BioB-3_at" not found' > sessionInfo() R version 2.9.1 (2009-06-26) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] grid stats graphics grDevices datasets utils methods [8] base other attached packages: [1] RODBC_1.2-5 bioDist_1.16.0 KernSmooth_2.23-2 [4] hthgu133a.db_2.2.11 RSQLite_0.7-1 DBI_0.2-4 [7] AnnotationDbi_1.6.1 genefilter_1.24.2 RColorBrewer_1.0-2 [10] gplots_2.7.1 caTools_1.9 bitops_1.0-4.1 [13] gdata_2.4.2 gtools_2.6.1 Biobase_2.4.1 [16] rcom_2.2-1 rscproxy_1.3-1 loaded via a namespace (and not attached): [1] annotate_1.22.0 splines_2.9.1 survival_2.35-4 xtable_1.5-5 The code works as expected using an eset derived from hgu133plus2 CEL files. Cheers, Fraser

Hi Fraser, I am afraid that you are unlucky on this one. The probe sequence that is coming up as not found is a newly added control sequence from Affymetrix (added this June). So it was not in the Affy files when we made the annotation package back in April. A newer package IS available however in the development branch right now. So you can use it today if you install R-devel and use biocLite(). Alternatively, you could wait a few weeks for the new release of R and bioconductor to go out. But whatever you do, do not attempt to use the newer annotation packages with the older version of Bioconductor. That will definitely NOT work. But installing a new R might be kind of a pain for you and its not your fault that Affy pulled a fast one on us. So I did some quick work for you to determine that the following probes are expected to be "extras" (because they were added by Affy last June). [1] "AFFX-BioB-3_at" "AFFX-BioB-5_at" "AFFX-BioB-M_at" "AFFX-BioC- 3_at" [5] "AFFX-BioC-5_at" "AFFX-BioDn-3_at" "AFFX-BioDn-5_at" "AFFX-CreX- 3_at" [9] "AFFX-CreX-5_at" So as a work around, I am betting that you probably just want to use the subset operator to remove those probes out of your ExpressionSet object before proceeding. Hope this helps, Marc Fraser Sim wrote: > Hi, > > I am having a problem running the following code which utilizes an eset > derived from hthgu133a CEL files. > > >> eset >> > ExpressionSet (storageMode: lockedEnvironment) > assayData: 13834 features, 9 samples > element names: exprs, se.exprs > phenoData > sampleNames: <<masked>> (9 total) > varLabels and varMetadata description: > sample: arbitrary numbering > CEL: NA > phenotype: NA > ShortName: NA > featureData > featureNames: 1007_s_at, 1053_at, ..., AFFX-r2-Ec-bioD-5_at (13834 total) > fvarLabels and fvarMetadata description: none > experimentData: use 'experimentData(object)' > Annotation: hthgu133a > > >> library(genefilter) >> nsF = nsFilter(eset, var.filter = FALSE)$eset >> > Error in .checkKeys(value, Lkeys(x), x at ifnotfound) : > value for "AFFX-BioB-3_at" not found' > > >> sessionInfo() >> > R version 2.9.1 (2009-06-26) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] grid stats graphics grDevices datasets utils methods > [8] base > > other attached packages: > [1] RODBC_1.2-5 bioDist_1.16.0 KernSmooth_2.23-2 > [4] hthgu133a.db_2.2.11 RSQLite_0.7-1 DBI_0.2-4 > [7] AnnotationDbi_1.6.1 genefilter_1.24.2 RColorBrewer_1.0-2 > [10] gplots_2.7.1 caTools_1.9 bitops_1.0-4.1 > [13] gdata_2.4.2 gtools_2.6.1 Biobase_2.4.1 > [16] rcom_2.2-1 rscproxy_1.3-1 > > loaded via a namespace (and not attached): > [1] annotate_1.22.0 splines_2.9.1 survival_2.35-4 xtable_1.5-5 > > The code works as expected using an eset derived from hgu133plus2 CEL files. > > Cheers, > Fraser > > _______________________________________________ > 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 > >