Hi, I have an ExpressionSetIllumina object with 12 samples. Is there a way to subset on the samples and create a new ExpressionSetIllumina object? The description of the ExpressionSetIllumina class has a combine() method for two ExpressionSetIllumina objects, and also has this: object[(index): Conducts subsetting of matrices and phenoData and reporterInfo components # shouldn't this read object[(index)]: ? It appears this subsetting works on the features, not samples: > dim(BS.bg.quant) Features Samples 45281 12 > temp <- BS.bg.quant[1:6] > dim(temp) Features Samples 6 12 Trying to subset on samples/columns like you can do for other ExpressionSet objects yields this: > temp <- BS.bg.quant[,1:6] Error: subscript out of bounds Is there a way to subset on samples, or is there a reason why I shouldn't subset the object but instead create a new one using readBeadSummaryData? Thanks, Jenny Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich@illinois.edu [[alternative HTML version deleted]]

Oops - I forgot my sessionInfo() > sessionInfo() R version 2.7.0 (2008-04-22) 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] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] beadarray_1.8.0 ath1121501probe_2.2.0 ath1121501cdf_2.2.0 [4] ath1121501.db_2.2.0 affyQCReport_1.18.0 geneplotter_1.18.0 [7] lattice_0.17-8 RColorBrewer_1.0-2 simpleaffy_2.16.0 [10] made4_1.14.0 ade4_1.4-7 affyPLM_1.16.0 [13] affycoretools_1.12.0 annaffy_1.12.0 KEGG.db_2.2.0 [16] gcrma_2.12.0 matchprobes_1.12.0 biomaRt_1.14.0 [19] RCurl_0.8-1 GOstats_2.6.0 Category_2.6.0 [22] genefilter_1.20.0 survival_2.34-1 RBGL_1.16.0 [25] annotate_1.18.0 xtable_1.5-2 GO.db_2.2.0 [28] AnnotationDbi_1.2.0 RSQLite_0.6-8 DBI_0.2-4 [31] graph_1.18.1 limma_2.14.1 affy_1.18.0 [34] preprocessCore_1.2.0 affyio_1.8.0 Biobase_2.0.1 [37] RWinEdt_1.8-0 loaded via a namespace (and not attached): [1] cluster_1.11.10 grid_2.7.0 KernSmooth_2.22-22 XML_1.94-0.1 > At 01:36 PM 5/22/2008, Jenny Drnevich wrote: >Hi, > >I have an ExpressionSetIllumina object with 12 samples. Is there a >way to subset on the samples and create a new ExpressionSetIllumina >object? The description of the ExpressionSetIllumina class has a >combine() method for two ExpressionSetIllumina objects, and also has this: > >object[(index): >Conducts subsetting of matrices and phenoData and reporterInfo components ># shouldn't this read object[(index)]: ? > >It appears this subsetting works on the features, not samples: > > > dim(BS.bg.quant) >Features Samples > 45281 12 > > > temp <- BS.bg.quant[1:6] > > dim(temp) >Features Samples > 6 12 > >Trying to subset on samples/columns like you can do for other >ExpressionSet objects yields this: > > > temp <- BS.bg.quant[,1:6] >Error: subscript out of bounds > > >Is there a way to subset on samples, or is there a reason why I >shouldn't subset the object but instead create a new one using >readBeadSummaryData? > >Thanks, >Jenny > > >Jenny Drnevich, Ph.D. > >Functional Genomics Bioinformatics Specialist >W.M. Keck Center for Comparative and Functional Genomics >Roy J. Carver Biotechnology Center >University of Illinois, Urbana-Champaign > >330 ERML >1201 W. Gregory Dr. >Urbana, IL 61801 >USA > >ph: 217-244-7355 >fax: 217-265-5066 >e-mail: drnevich at illinois.edu > [[alternative HTML version deleted]] > >_______________________________________________ >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

Hi Jenny, Sorry to hear that subsetting isn¹t quite working as you would expect. Using the example data set available with the beadarray package I am able to subset probes/samples in the usual way without error. Do the following commands work ok for you? Best wishes, Matt > library(beadarray) > data(BSData) > dim(BSData) Features Samples 47312 18 > sub1 = BSData[,1:6] > dim(sub1) Features Samples 47312 6 > sub2 = BSData[1:6,] > dim(sub2) Features Samples 6 18 > sub3 = BSData[11:20,4:7] > dim(sub3) Features Samples 10 4 > sessionInfo() R version 2.7.0 (2008-04-22) i386-apple-darwin8.10.1 locale: en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] tools stats graphics grDevices utils datasets methods base other attached packages: [1] beadarray_1.8.0 affy_1.18.0 preprocessCore_1.2.0 affyio_1.8.0 [5] geneplotter_1.18.0 annotate_1.18.0 xtable_1.5-2 AnnotationDbi_1.2.0 [9] RSQLite_0.6-8 DBI_0.2-4 lattice_0.17-6 Biobase_2.0.0 [13] limma_2.14.0 loaded via a namespace (and not attached): [1] KernSmooth_2.22-22 RColorBrewer_1.0-2 grid_2.7.0 On 22/5/08 19:36, "Jenny Drnevich" <drnevich@illinois.edu> wrote: > Hi, > > I have an ExpressionSetIllumina object with 12 samples. Is there a way to > subset on the samples and create a new ExpressionSetIllumina object? The > description of the ExpressionSetIllumina class has a combine() method for two > ExpressionSetIllumina objects, and also has this: > > object[(index): Conducts subsetting of matrices and phenoData and reporterInfo > components # shouldn't this read object[(index)]: ? > > It appears this subsetting works on the features, not samples: > >> > dim(BS.bg.quant) > Features Samples > 45281 12 > >> > temp <- BS.bg.quant[1:6] >> > dim(temp) > Features Samples > 6 12 > > Trying to subset on samples/columns like you can do for other ExpressionSet > objects yields this: > >> > temp <- BS.bg.quant[,1:6] > Error: subscript out of bounds > > > Is there a way to subset on samples, or is there a reason why I shouldn't > subset the object but instead create a new one using readBeadSummaryData? > > Thanks, > Jenny [[alternative HTML version deleted]]