exonmap question: rma (& plier) crashes
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@tae-hoon-chung-2994
Last seen 8.4 years ago
Hi, All; I simply followed the exonmap vignette but came up with an unexpected error. Here are what I did: > library(exonmap) Loading required package: affy 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: affyio Loading required package: preprocessCore Loading required package: simpleaffy Loading required package: genefilter Loading required package: survival Loading required package: splines Loading required package: gcrma Loading required package: matchprobes Loading required package: RColorBrewer Loading required package: RMySQL Loading required package: DBI Loading required package: plier > raw <- read.exon(covdesc='design.csv') > raw@cdfName <- "exon.pmcdf" > dat.rma <- rma(raw) Error in .local(object, ...) : subscript out of bounds > sessionInfo() R version 2.7.2 beta (2008-08-16 r46368) i386-apple-darwin9.4.0 locale: C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] exon.pmcdf_1.1 exonmap_1.6.05 plier_1.8.0 [4] RMySQL_0.6-0 DBI_0.2-4 RColorBrewer_1.0-2 [7] simpleaffy_2.14.05 gcrma_2.12.1 matchprobes_1.12.0 [10] genefilter_1.20.0 survival_2.34-1 affy_1.16.0 [13] preprocessCore_1.0.0 affyio_1.6.1 Biobase_2.0.1 loaded via a namespace (and not attached): [1] AnnotationDbi_1.0.6 RSQLite_0.6-4 annotate_1.18.0 Thanks in advance; Tae-Hoon -- Tae-Hoon Chung Korea Centers for Disease Control & Prevention (KCDC) Korea National Institute of Health Center for Genome Sciences :: Biobank Team (T) +82-2-380-2252 (F) +82-2-354-1078 (M) +82-10-3511-1012 [[alternative HTML version deleted]]
exonmap exonmap • 704 views
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Crispin Miller ★ 1.1k
@crispin-miller-264
Last seen 8.4 years ago
Hi, It looks like the issue is happening somewhere in rma() - or something it doesn¹t like in the Oraw¹ data object... There¹s a more recent version of the affy library than the one you¹re using, I think. Please can you try updating that and seeing if it fixes things? Crispin On 19/8/08 09:15, "" <> wrote: > Hi, All; > > I simply followed the exonmap vignette but came up with an unexpected > error. > Here are what I did: > >> > library(exonmap) > Loading required package: affy > 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: affyio > Loading required package: preprocessCore > Loading required package: simpleaffy > Loading required package: genefilter > Loading required package: survival > Loading required package: splines > Loading required package: gcrma > Loading required package: matchprobes > Loading required package: RColorBrewer > Loading required package: RMySQL > Loading required package: DBI > Loading required package: plier > >> > raw <- read.exon(covdesc='design.csv') >> > raw@cdfName <- "exon.pmcdf" >> > dat.rma <- rma(raw) > Error in .local(object, ...) : subscript out of bounds >> > sessionInfo() > R version 2.7.2 beta (2008-08-16 r46368) > i386-apple-darwin9.4.0 > > locale: > C > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] exon.pmcdf_1.1 exonmap_1.6.05 plier_1.8.0 > [4] RMySQL_0.6-0 DBI_0.2-4 RColorBrewer_1.0-2 > [7] simpleaffy_2.14.05 gcrma_2.12.1 matchprobes_1.12.0 > [10] genefilter_1.20.0 survival_2.34-1 affy_1.16.0 > [13] preprocessCore_1.0.0 affyio_1.6.1 Biobase_2.0.1 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.0.6 RSQLite_0.6-4 annotate_1.18.0 > > Thanks in advance; > > Tae-Hoon > > -- > Tae-Hoon Chung > > Korea Centers for Disease Control & Prevention (KCDC) > Korea National Institute of Health > Center for Genome Sciences :: Biobank Team > > (T) +82-2-380-2252 > (F) +82-2-354-1078 > (M) +82-10-3511-1012 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -------------------------------------------------------- This email is confidential and intended solely for the u...{{dropped:15}}
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