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exonmap question: rma (& plier ) crashes conti.

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Tae-Hoon Chung ▴ 70

@tae-hoon-chung-2994

Last seen 9.6 years ago

Hi, All; I posted this question and someone suggested to update my bioconductor packages and retry. I did and retried but failed again: > 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 > setwd('~/KCDC/LCL-microarray/scandata') > 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_1.10.0 [4] RMySQL_0.6-0 DBI_0.2-4 RColorBrewer_1.0-2 [7] simpleaffy_2.16.0 gcrma_2.12.1 matchprobes_1.12.0 [10] genefilter_1.20.0 survival_2.34-1 affy_1.18.2 [13] preprocessCore_1.2.1 affyio_1.8.1 Biobase_2.0.1 loaded via a namespace (and not attached): [1] AnnotationDbi_1.2.2 RSQLite_0.6-9 annotate_1.18.0 The same problem occurred with both the "exon.pmcdf" and "huex10stv2hsentrezgcdf" annotation packages: > raw@cdfName <- "huex10stv2hsentrezgcdf" > dat.rma <- rma(raw) Attaching package: 'huex10stv2hsentrezgcdf' The following object(s) are masked from package:exon.pmcdf : i2xy, xy2i Error in .local(object, ...) : subscript out of bounds Anyone any suggestions? I really don't know whether this is the problem of annotation packages or rma function or something else! 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]]

Annotation cdf Annotation cdf • 1.1k views

ADD COMMENT • link 15.7 years ago Tae-Hoon Chung ▴ 70

score 0 · Answer 1 · 2008-08-20

Hi, All; I posted this question and someone suggested to update my bioconductor packages and retry. I did and retried but failed again: > 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 > setwd('~/KCDC/LCL-microarray/scandata') > 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_1.10.0 [4] RMySQL_0.6-0 DBI_0.2-4 RColorBrewer_1.0-2 [7] simpleaffy_2.16.0 gcrma_2.12.1 matchprobes_1.12.0 [10] genefilter_1.20.0 survival_2.34-1 affy_1.18.2 [13] preprocessCore_1.2.1 affyio_1.8.1 Biobase_2.0.1 loaded via a namespace (and not attached): [1] AnnotationDbi_1.2.2 RSQLite_0.6-9 annotate_1.18.0 When I traced the source of the error, I got the following result: > traceback() 4: .local(object, ...) 3: pm(object, subset) 2: pm(object, subset) 1: rma(raw) The problem occurred at the .local function of the following method definition: > showMethods("pm", class="AffyBatch", includeDef=T) Function: pm (package affy) object="AffyBatch" function (object, ...) { .local <- function (object, genenames = NULL, LISTRUE = FALSE) { if (is.null(genenames) & !LISTRUE) { cdfname <- getCdfInfo(object) psets <- as.list(cdfname) psets <- psets[order(names(psets))] index <- unlist(sapply(psets, function(x) x[, 1]), use.names = FALSE) return(exprs(object)[index, , drop = FALSE]) } else { return(probes(object, "pm", genenames, LISTRUE = LISTRUE)) } } .local(object, ...) } When I followed the steps in the .local function definition myself, I got the following result: > psets <- as.list(getCdfInfo(raw))> psets <- psets[order(names(psets))] > index <- unlist(sapply(psets, function(x) x[,1]), use.names=F) > length(index) [1] 1164743 > dim(exprs(raw)) [1] 1102500 39 > mat <- exprs(raw)[index, , drop=F] Error: subscript out of bounds No suitable frames for recover() >From this, it is obvious that "subscript out of bounds" error happened. (Of course!) Is the annotation package at fault or the "pm" method at fault or both or neither of them at fault? When I used the "huex10stv2hsentrezgcdf" annotation package instead of the "exon.pmcdf" annotation package, the same error occurred. 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]]