Question: Cannot Subset Columns in beadarray package, ExpressionSetIllumina Class in R-2.8.0, BioBase 2.2.1, beadarray 1.10.0
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gravatar for Julian Lee
10.9 years ago by
Julian Lee140
Julian Lee140 wrote:
Hi Mark and Others, I'm having some problems with the new beadarray package. I can't subset the columns, Example >library(beadarray) Loading required package: limma Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: geneplotter Loading required package: lattice Loading required package: annotate Loading required package: AnnotationDbi Loading required package: xtable KernSmooth 2.22 installed Copyright M. P. Wand 1997 Loading required package: hwriter Loading required package: sma Attaching package: 'beadarray' The following object(s) are masked from package:limma : backgroundCorrect, imageplot, plotMA > data(BSData) > BSData ExpressionSetIllumina (storageMode: list) assayData: 1471 features, 10 samples element names: exprs, se.exprs, NoBeads phenoData rowNames: 1318758_R007_C004, 1318791_R002_C006, ..., 1318758_R002_C002 (10 total) varLabels and varMetadata description: arrayName: NA featureData featureNames: 2, 3, ..., 6140 (1471 total) fvarLabels and fvarMetadata description: ProbeID: NA experimentData: use 'experimentData(object)' Annotation: illuminaProbeIDs QC Information Available Slots: exprs se.exprs NoBeads controlType featureNames: sampleNames: > BSData[,1:2] Error: subscript out of bounds ##Other Examples > dataFile<-'for_R.txt' > sampleSheet<-'SampleSheet.csv' > readBeadSummaryData(dataFile=dataFile,skip=0,ProbeID='TargetID',samp leSheet=sampleSheet)->BSData2 > BSData2 ExpressionSetIllumina (storageMode: list) assayData: 27578 features, 24 samples element names: exprs, se.exprs, NoBeads, Detection phenoData rowNames: AGS, AZ521, ..., Methylated (24 total) varLabels and varMetadata description: Sample_Name: Sample_Name Sample_Well: Sample_Well ...: ... Unique: Unique (8 total) featureData featureNames: cg00000292, cg00002426, ..., cg27665659 (27578 total) fvarLabels and fvarMetadata description: ProbeID: NA experimentData: use 'experimentData(object)' Annotation: QC Information Available Slots: exprs se.exprs NoBeads controlType featureNames: sampleNames: > BSData2[,1:2] Error: subscript out of bounds No errors are reported while reading the data into R. However, this works on my older Windows R-2.7.1 on Beadarray 1.8.0. ps - Katrina Bell, if you're reading this, I'm playing with the new Infinium 27k methylation dataset. regards julian > sessionInfo() R version 2.8.0 (2008-10-20) i486-pc-linux-gnu locale: LC_CTYPE=en_SG.UTF-8;LC_NUMERIC=C;LC_TIME=en_SG.UTF-8;LC_COLLATE=en_SG .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_SG.UTF-8;LC_PAPER=en_SG.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_SG.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] beadarray_1.10.0 sma_0.5.15 hwriter_0.93 [4] geneplotter_1.20.0 annotate_1.20.1 xtable_1.5-4 [7] AnnotationDbi_1.4.2 lattice_0.17-17 Biobase_2.2.1 [10] limma_2.16.3 loaded via a namespace (and not attached): [1] DBI_0.2-4 grid_2.8.0 KernSmooth_2.22-22 RColorBrewer_1.0-2 [5] RSQLite_0.7-1 -- Julian Lee Bioinformatics Specialist Cellular and Molecular Research National Cancer Center Singapore
cancer beadarray • 603 views
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