Tonight one of my functions suddenly stopped working and I have traced the problem to not being able to subset esets by row as I previously could. Thus, eset[1:5,] yields an error "subscript out of bounds", whereas, eset[,1:5] does not. See below for a concrete example with output and sessionInfo(). Thanks, Mark > eset Expression Set (exprSet) with 119 genes 59 samples phenoData object with 4 variables and 59 cases varLabels sampleNames: read from file Strain: read from file Region: read from file Animal: read from file > eset[1:5,] Error in eset[1:5, ] : subscript out of bounds > eset[,1:5] Expression Set (exprSet) with 119 genes 5 samples phenoData object with 4 variables and 5 cases varLabels sampleNames: read from file Strain: read from file Region: read from file Animal: read from file > exprs(eset)[1:5, 1:5] WS02R111.CEL WS02R112.CEL WS02R113.CEL WS02R114.CEL WS02R115.CEL L07074_at 10.218309 10.270285 10.502409 10.735885 10.374594 U53873cds_at 6.589952 6.720901 6.503514 6.347453 6.507239 M85193_at 9.341253 9.159996 9.116925 9.184803 9.170827 U72349_at 8.169101 7.628983 8.136620 7.878559 8.049834 rc_AA800265_at 6.603026 6.621253 5.902590 6.437841 6.394334 > sessionInfo() Version 2.3.0 (2006-04-24) i386-pc-mingw32 attached base packages: [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" "utils" "datasets" "base" other attached packages: genefilter rgu34a multtest survival affy affyio Biobase RWinEdt "1.10.1" "1.12.0" "1.9.5" "2.24" "1.10.0" "1.0.0" "1.10.0" "1.7-4" Mark W. Kimpel MD ? Official Business Address: ? Department of Psychiatry Indiana University School of Medicine Biotechnology, Research, & Training Center 1345 W. 16th Street Indianapolis, IN ?46202 ? Preferred Mailing Address: ? 15032 Hunter Court Westfield, IN? 46074 ? (317) 490-5129 Home, Work, & Mobile 1-(317)-536-2730 FAX

Hi Mark -- The basic functionality works in Biobase > sessionInfo() Version 2.3.0 Patched (2006-04-24 r37913) x86_64-unknown-linux-gnu attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: Biobase "1.10.0" > data(sample.exprSet) > sample.exprSet[1:5,] Expression Set (exprSet) with 5 genes 26 samples phenoData object with 3 variables and 26 cases varLabels sex: Female/Male type: Case/Control score: Testing Score so the problem is a little deeper. Other elements of your exprSet may be malformed. The following should both work: se.exprs(sample.exprSet)[1:5,] reporterInfo(sample.exprSet)[1:5,] My guess is that it's the se.exprs that is causing problems. If these measures are unimportant, then, in your case, se.exprs(eset) <- matrix(nrow=0,ncol=59) will replace what you currently have with a matrix that indicates to exprSet that it has no information. If the se.exprs *are* important, then we'll need more information about how the exprSet was created, to figure out where the malformed entry is coming from. Hope that helps. Martin -- Bioconductor "Kimpel, Mark William" <mkimpel at="" iupui.edu=""> writes: > Tonight one of my functions suddenly stopped working and I have > traced the problem to not being able to subset esets by row as I > previously could. Thus, eset[1:5,] yields an error "subscript out of > bounds", whereas, eset[,1:5] does not. See below for a concrete > example with output and sessionInfo(). Thanks, Mark > >> eset > Expression Set (exprSet) with > 119 genes > 59 samples > phenoData object with 4 variables and 59 cases > varLabels > sampleNames: read from file > Strain: read from file > Region: read from file > Animal: read from file >> eset[1:5,] > Error in eset[1:5, ] : subscript out of bounds >> eset[,1:5] > Expression Set (exprSet) with > 119 genes > 5 samples > phenoData object with 4 variables and 5 cases > varLabels > sampleNames: read from file > Strain: read from file > Region: read from file > Animal: read from file >> exprs(eset)[1:5, 1:5] > WS02R111.CEL WS02R112.CEL WS02R113.CEL WS02R114.CEL WS02R115.CEL > L07074_at 10.218309 10.270285 10.502409 10.735885 10.374594 > U53873cds_at 6.589952 6.720901 6.503514 6.347453 6.507239 > M85193_at 9.341253 9.159996 9.116925 9.184803 9.170827 > U72349_at 8.169101 7.628983 8.136620 7.878559 8.049834 > rc_AA800265_at 6.603026 6.621253 5.902590 6.437841 6.394334 >> sessionInfo() > Version 2.3.0 (2006-04-24) > i386-pc-mingw32 > > attached base packages: > [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" "utils" "datasets" "base" > > other attached packages: > genefilter rgu34a multtest survival affy affyio Biobase RWinEdt > "1.10.1" "1.12.0" "1.9.5" "2.24" "1.10.0" "1.0.0" "1.10.0" "1.7-4" > Mark W. Kimpel MD > > ? > Official Business Address: > ? > Department of Psychiatry > Indiana University School of Medicine > Biotechnology, Research, & Training Center > 1345 W. 16th Street > Indianapolis, IN ?46202 > ? > Preferred Mailing Address: > ? > 15032 Hunter Court > Westfield, IN? 46074 > ? > (317) 490-5129 Home, Work, & Mobile > 1-(317)-536-2730 FAX > > _______________________________________________ > 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

Martin, you were correct. I had performed an operation that corrupted the se.exprs slot. Since I never use this, I had forgotten about it. Thanks, Mark Mark W. Kimpel MD (317) 490-5129 Home, Work, & Mobile 1-(317)-536-2730 FAX -----Original Message----- From: Martin Morgan [mailto:mtmorgan@fhcrc.org] Sent: Saturday, May 13, 2006 10:24 AM To: Kimpel, Mark William Cc: Bioconductor Newsgroup Subject: Re: [BioC] subset eset by row broken Hi Mark -- The basic functionality works in Biobase > sessionInfo() Version 2.3.0 Patched (2006-04-24 r37913) x86_64-unknown-linux-gnu attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: Biobase "1.10.0" > data(sample.exprSet) > sample.exprSet[1:5,] Expression Set (exprSet) with 5 genes 26 samples phenoData object with 3 variables and 26 cases varLabels sex: Female/Male type: Case/Control score: Testing Score so the problem is a little deeper. Other elements of your exprSet may be malformed. The following should both work: se.exprs(sample.exprSet)[1:5,] reporterInfo(sample.exprSet)[1:5,] My guess is that it's the se.exprs that is causing problems. If these measures are unimportant, then, in your case, se.exprs(eset) <- matrix(nrow=0,ncol=59) will replace what you currently have with a matrix that indicates to exprSet that it has no information. If the se.exprs *are* important, then we'll need more information about how the exprSet was created, to figure out where the malformed entry is coming from. Hope that helps. Martin -- Bioconductor "Kimpel, Mark William" <mkimpel at="" iupui.edu=""> writes: > Tonight one of my functions suddenly stopped working and I have > traced the problem to not being able to subset esets by row as I > previously could. Thus, eset[1:5,] yields an error "subscript out of > bounds", whereas, eset[,1:5] does not. See below for a concrete > example with output and sessionInfo(). Thanks, Mark > >> eset > Expression Set (exprSet) with > 119 genes > 59 samples > phenoData object with 4 variables and 59 cases > varLabels > sampleNames: read from file > Strain: read from file > Region: read from file > Animal: read from file >> eset[1:5,] > Error in eset[1:5, ] : subscript out of bounds >> eset[,1:5] > Expression Set (exprSet) with > 119 genes > 5 samples > phenoData object with 4 variables and 5 cases > varLabels > sampleNames: read from file > Strain: read from file > Region: read from file > Animal: read from file >> exprs(eset)[1:5, 1:5] > WS02R111.CEL WS02R112.CEL WS02R113.CEL WS02R114.CEL WS02R115.CEL > L07074_at 10.218309 10.270285 10.502409 10.735885 10.374594 > U53873cds_at 6.589952 6.720901 6.503514 6.347453 6.507239 > M85193_at 9.341253 9.159996 9.116925 9.184803 9.170827 > U72349_at 8.169101 7.628983 8.136620 7.878559 8.049834 > rc_AA800265_at 6.603026 6.621253 5.902590 6.437841 6.394334 >> sessionInfo() > Version 2.3.0 (2006-04-24) > i386-pc-mingw32 > > attached base packages: > [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" "utils" "datasets" "base" > > other attached packages: > genefilter rgu34a multtest survival affy affyio Biobase RWinEdt > "1.10.1" "1.12.0" "1.9.5" "2.24" "1.10.0" "1.0.0" "1.10.0" "1.7-4" > Mark W. Kimpel MD > > ? > Official Business Address: > ? > Department of Psychiatry > Indiana University School of Medicine > Biotechnology, Research, & Training Center > 1345 W. 16th Street > Indianapolis, IN ?46202 > ? > Preferred Mailing Address: > ? > 15032 Hunter Court > Westfield, IN? 46074 > ? > (317) 490-5129 Home, Work, & Mobile > 1-(317)-536-2730 FAX > > _______________________________________________ > 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