Possible bug in SNPchip
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@francesco-mancuso-4483
Last seen 8.4 years ago
Hi all! I have some problems using SNPchip package. When i run the following code > oligoSet <- new("oligoSnpSet", copyNumber=as.matrix(CopyNumber), call=crlmmCalls, callProbability=crlmmConf, annotation=annotation(crlmmOut)) > x <- oligoSet[chromosome(oligoSet) %in% as.character(3), c(1,2)] > plot(x) I obtain the following error: Error in plotCytoband(cytoband = cytoband, new = FALSE, cytoband.ycoords = op$cytoband.ycoords, : subscript out of bounds The strange is that if I plot only chromosome 1 (or a set of chromosome that start from 1), it works. I really would appreciate any help! Best, Francesco This is my R session info R version 2.14.0 (2011-10-31) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] 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] grDevices datasets splines graphics stats tcltk utils methods base other attached packages: [1] crlmm_1.12.0 SNPchip_1.18.0 VanillaICE_1.16.1 IRanges_1.12.1 pd.mapping250k.sty_1.4.0 RSQLite_0.10.0 DBI_0.2-5 oligo_1.18.0 oligoClasses_1.16.0 [10] Biobase_2.14.0 svSocket_0.9-52 TinnR_1.0.3 R2HTML_2.2 Hmisc_3.9-0 survival_2.36-10 loaded via a namespace (and not attached): [1] affxparser_1.26.1 affyio_1.22.0 annotate_1.32.0 AnnotationDbi_1.16.0 Biostrings_2.22.0 bit_1.1-7 cluster_1.14.1 ellipse_0.3-5 ff_2.2-3 genefilter_1.36.0 [11] grid_2.14.0 lattice_0.20-1 mvtnorm_0.9-9991 preprocessCore_1.16.0 svMisc_0.9-63 tools_2.14.0 xtable_1.6-0 zlibbioc_1.0.0 -- *Francesco Mattia Mancuso* Bioinformatician - Bioinformatics Core Facility - Proteomics Core Facility CRG-Centre for Genomic Regulation (Room 439) C/ Dr. Aiguader, 88 (Edif. PRBB) 08003 Barcelona, Spain Mail: francesco.mancuso@crg.eu <mailto:francesco.mancuso@crg.eu> Phone: +34 933160202 http://www.crg.es/bioinformatics_unit [[alternative HTML version deleted]]
Proteomics SNPchip Proteomics SNPchip • 735 views
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Rob Scharpf ▴ 250
@rob-scharpf-1931
Last seen 8.4 years ago
On Nov 16, 2011, at 6:00 AM, bioconductor-request@r-project.org wrote: > Message: 1 > Date: Tue, 15 Nov 2011 13:20:15 +0100 > From: Francesco Mancuso <francesco.mancuso@crg.eu> > To: <bioconductor@r-project.org> > Subject: [BioC] Possible bug in SNPchip > Message-ID: <4EC258FF.5020205@crg.eu> > Content-Type: text/plain > > Hi all! > I have some problems using SNPchip package. > > When i run the following code >> oligoSet <- new("oligoSnpSet", copyNumber=as.matrix(CopyNumber), > call=crlmmCalls, callProbability=crlmmConf, annotation=annotation(crlmmOut)) >> x <- oligoSet[chromosome(oligoSet) %in% as.character(3), c(1,2)] >> plot(x) > I obtain the following error: > > Error in plotCytoband(cytoband = cytoband, new = FALSE, cytoband.ycoords = op$cytoband.ycoords, : > subscript out of bounds > > > The strange is that if I plot only chromosome 1 (or a set of chromosome > that start from 1), it works. Fixed in v 1.18.1 on the release branch, as well as devel (v.19.1). Thanks- Rob > This is my R session info > > R version 2.14.0 (2011-10-31) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] 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] grDevices datasets splines graphics stats tcltk utils methods base > > other attached packages: > [1] crlmm_1.12.0 SNPchip_1.18.0 VanillaICE_1.16.1 IRanges_1.12.1 pd.mapping250k.sty_1.4.0 RSQLite_0.10.0 DBI_0.2-5 oligo_1.18.0 oligoClasses_1.16.0 > [10] Biobase_2.14.0 svSocket_0.9-52 TinnR_1.0.3 R2HTML_2.2 Hmisc_3.9-0 survival_2.36-10 > > loaded via a namespace (and not attached): > [1] affxparser_1.26.1 affyio_1.22.0 annotate_1.32.0 AnnotationDbi_1.16.0 Biostrings_2.22.0 bit_1.1-7 cluster_1.14.1 ellipse_0.3-5 ff_2.2-3 genefilter_1.36.0 > [11] grid_2.14.0 lattice_0.20-1 mvtnorm_0.9-9991 preprocessCore_1.16.0 svMisc_0.9-63 tools_2.14.0 xtable_1.6-0 zlibbioc_1.0.0 > > > > -- > > *Francesco Mattia Mancuso* > Bioinformatician > > - Bioinformatics Core Facility > - Proteomics Core Facility > > CRG-Centre for Genomic Regulation (Room 439) > C/ Dr. Aiguader, 88 (Edif. PRBB) > 08003 Barcelona, Spain [[alternative HTML version deleted]]
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