I am using rowQ to filter on interquartile range on HgU133 plus2 Affy chips. The following is my setup and a description of the ExpressionSet, and at the end, the error I'm getting "which is larger than the number of rows" which is, of course, not true since both 13669 and 41006 are less than 54675, the number of rows in the ExpressionSet. > sessionInfo() R version 2.6.0 (2007-10-03) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en _US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_ US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UT F-8;LC_IDENTIFICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] vsn_3.2.1 limma_2.12.0 geneplotter_1.16.0 [4] lattice_0.17-4 annotate_1.16.1 xtable_1.5-2 [7] AnnotationDbi_1.0.6 RSQLite_0.6-4 DBI_0.2-4 [10] hgu133plus2cdf_2.0.0 affy_1.16.0 preprocessCore_1.0.0 [13] affyio_1.6.1 Biobase_1.16.1 loaded via a namespace (and not attached): [1] grid_2.6.0 KernSmooth_2.22-21 RColorBrewer_1.0-2 rcompgen_0.1-17 > CHT_veset ExpressionSet (storageMode: lockedEnvironment) assayData: 54675 features, 29 samples element names: exprs phenoData sampleNames: T1_S13.CEL, T1_S15.CEL, ..., T5_S8.CEL (29 total) varLabels and varMetadata description: sample: arbitrary numbering featureData featureNames: 1007_s_at, 1053_at, ..., AFFX-TrpnX-M_at (54675 total) fvarLabels and fvarMetadata description: none experimentData: use 'experimentData(object)' Annotation: hgu133plus2 > lowQ<-rowQ(exprs(CHT_veset), floor(13669)) Error in rowQ(exprs(CHT_veset), floor(13669)) : which is larger than the number of rows > upQ<-rowQ(CHT_veset, ceiling(41006)) Error in rowQ(exprs(imat), which) : which is larger than the number of rows Dennis Burian, Ph.D. Functional Genomics Group Civil Aerospace Medical Institute, AAM-610 6500 S. MacArthur Blvd. Oklahoma City OK 73169 405-954-6087 dennis.burian at faa.gov

Hi Dennis, Dennis.Burian at faa.gov wrote: > I am using rowQ to filter on interquartile range on HgU133 plus2 Affy > chips. The following is my setup and a description of the ExpressionSet, > and at the end, the error I'm getting "which is larger than the number of > rows" which is, of course, not true since both 13669 and 41006 are less > than 54675, the number of rows in the ExpressionSet. > > > sessionInfo() > R version 2.6.0 (2007-10-03) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE= en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=e n_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US. UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] vsn_3.2.1 limma_2.12.0 geneplotter_1.16.0 > [4] lattice_0.17-4 annotate_1.16.1 xtable_1.5-2 > [7] AnnotationDbi_1.0.6 RSQLite_0.6-4 DBI_0.2-4 > [10] hgu133plus2cdf_2.0.0 affy_1.16.0 preprocessCore_1.0.0 > [13] affyio_1.6.1 Biobase_1.16.1 > > loaded via a namespace (and not attached): > [1] grid_2.6.0 KernSmooth_2.22-21 RColorBrewer_1.0-2 > rcompgen_0.1-17 > > CHT_veset > ExpressionSet (storageMode: lockedEnvironment) > assayData: 54675 features, 29 samples > element names: exprs > phenoData > sampleNames: T1_S13.CEL, T1_S15.CEL, ..., T5_S8.CEL (29 total) > varLabels and varMetadata description: > sample: arbitrary numbering > featureData > featureNames: 1007_s_at, 1053_at, ..., AFFX-TrpnX-M_at (54675 total) > fvarLabels and fvarMetadata description: none > experimentData: use 'experimentData(object)' > Annotation: hgu133plus2 > > lowQ<-rowQ(exprs(CHT_veset), floor(13669)) rowQ is computing the quantiles for the row, so you only have 29 observations. The error is trying to tell you that. If you want to filter so that you choose the 13669 rows with the largest IQRs (or something like that) you should use the nsFilter function. nsFilter also takes care of duplicate EntrezGene IDs (if you want it to). (and as an aside, you can just do: lowQ<-rowQ(CHT_veset, 13) or lowQ<-rowQ(CHT_vest, 13L) if you are really wanting to be careful) hope that helps Robert > Error in rowQ(exprs(CHT_veset), floor(13669)) : > which is larger than the number of rows > > upQ<-rowQ(CHT_veset, ceiling(41006)) > Error in rowQ(exprs(imat), which) : > which is larger than the number of rows > > Dennis Burian, Ph.D. > Functional Genomics Group > Civil Aerospace Medical Institute, AAM-610 > 6500 S. MacArthur Blvd. > Oklahoma City OK 73169 > 405-954-6087 > dennis.burian at faa.gov > > _______________________________________________ > 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 > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org