Dear list, I am trying to follow the new bead-summary tutorial http://www.bioconductor.org/packages/release/bioc/vignettes/beadarray/ inst/doc/beadsummary.pdf However, I end up with a ‘subscript out of bounds’ error. Does anyone happen to know what´s wrong? > library(beadarray) Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Welcome to beadarray version 2.0.1 There have been major changes to beadarray since Bioconductor 2.6 (April 2010). Please see package vignette for details > dataFile = "AsuragenMAQC-probe-raw.txt" > qcFile = "AsuragenMAQC-controls.txt" > BSData = readBeadSummaryData(dataFile = dataFile, qcFile = qcFile, controlID = "ProbeID", skip = 0, qc.skip = 0, qc.columns = list(exprs = "AVG_Signal",Detection = "Detection Pval")) Warning message: In readQC(file = qcFile, sep = qc.sep, skip = qc.skip, columns = qc.columns, : controlIDs non-unique: 6 repeated entries have been removed. > BSData ExpressionSetIllumina (storageMode: list) Error in object@channelData[[1]] : subscript out of bounds > sessionInfo() R version 2.12.0 (2010-10-15) Platform: i386-apple-darwin9.8.0/i386 (32-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] beadarray_2.0.1 Biobase_2.10.0 loaded via a namespace (and not attached): [1] limma_3.6.6 > Many thanks, cheers, Moritz Moritz Kebschull Fellow Clinical Research Unit 208 University of Bonn, Germany [[alternative HTML version deleted]]

Hi Moritz, Thanks for your report. The problem was caused by readBeadSummary data not correctly setting the channelData slot of the ExpressionSetIllumina class, so the dimensions of the object could not be displayed properly. The bug should be fixed now and will appear in an updated version of the package in the next day or so. In fact. the only consequence of the bug is the way that the object is displayed. The rest of the vignette should work fine. Regards, Mark On Thu, Nov 4, 2010 at 10:17 AM, Moritz Kebschull <endothel at="" gmail.com=""> wrote: > Dear list, > > I am trying to follow the new bead-summary tutorial > > http://www.bioconductor.org/packages/release/bioc/vignettes/beadarra y/inst/doc/beadsummary.pdf > > However, I end up with a ?subscript out of bounds? error. Does anyone happen > to know what?s wrong? > >> library(beadarray) > Loading required package: Biobase > > Welcome to Bioconductor > > ?Vignettes contain introductory material. To view, type > ?'openVignette()'. To cite Bioconductor, see > ?'citation("Biobase")' and for packages 'citation(pkgname)'. > > Welcome to beadarray version 2.0.1 > There have been major changes to beadarray since Bioconductor 2.6 (April > 2010). Please see package vignette for details >> dataFile = "AsuragenMAQC-probe-raw.txt" >> qcFile = "AsuragenMAQC-controls.txt" >> BSData = readBeadSummaryData(dataFile = dataFile, qcFile = qcFile, > controlID = "ProbeID", skip = 0, qc.skip = 0, qc.columns = list(exprs = > "AVG_Signal",Detection = "Detection Pval")) > Warning message: > In readQC(file = qcFile, sep = qc.sep, skip = qc.skip, columns = qc.columns, > ?: > ?controlIDs non-unique: 6 repeated entries have been removed. > >> BSData > ExpressionSetIllumina (storageMode: list) > Error in object at channelData[[1]] : subscript out of bounds >> sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: i386-apple-darwin9.8.0/i386 (32-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] beadarray_2.0.1 Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] limma_3.6.6 >> > > Many thanks, > > cheers, Moritz > > > Moritz Kebschull > Fellow > Clinical Research Unit 208 > University of Bonn, Germany > > ? ? ? ?[[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 >