[BioC] exonmap question: rma (& plier ) crashes conti.
Michal Okoniewski
michal.okoniewski at fgcz.ethz.ch
Mon Aug 25 17:57:28 CEST 2008
Hi Tae-Hoon,
The numbers that you get from the size of raw data is strange - for exon
chip there should be 6553600 rows.
Hmmm... sure that you read in are exon chip CEL files?
The number of probesets in the exon.pmcdf is also different - there are
normally 1411189.
Cheers,
Michal
Tae-Hoon Chung wrote:
> 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 at 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
>
>
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