rma subscript out of bounds with Rat Exon data

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Rob Dunne ▴ 230

@rob-dunne-292

Last seen 9.6 years ago

Hello Bioconductor list, I get an error when I try to rma normalize a data set of Rat Exon 1.0 ST cel files i.e. library(exonmap) library(ratexonpmcdf) # Rat Exon 1.0ST from #http://xmap.picr.man.ac.uk/download/ data<-read.exon(path="/home/bioinfo/RatDiet/",compress=TRUE) data at cdfName #[1] "RaGene-1_0-st-v1" data at cdfName <- "ratexonpmcdf" X<-rma(data) #Error in .local(object, ...) : subscript out of bounds length(probeNames(data)) #3999056 length(data) #59 length(geneNames(data)) #1018777 The problem occurs in the "pm" function where it appears that an index is generated that is much larger than the matrix of expression values. I have no problems with the human array tutorial example provided at http://bioinformatics.picr.man.ac.uk/ Bye Rob

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ADD COMMENT • link updated 16.0 years ago by Crispin Miller ★ 1.1k • written 16.0 years ago by Rob Dunne ▴ 230

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Hi Rob,

I am having the similar problem while using my custom cdf. I get the following error while using rma.

Error in exprs(object)[index, , drop = FALSE] : subscript out of bounds

How did you solve yours?

Thanks,

Pas

ADD REPLY • link 6.3 years ago PAS • 0

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Crispin Miller ★ 1.1k

@crispin-miller-264

Last seen 9.6 years ago

Hi Rob, That's curious... Please can you let us know which versions of the software you're running with a call to: > sessionInfo() -- and what platform (i.e. Linux, Windows, Mac OS X ...) you're running on. Do you get the same error if you call read.exon() from the directory with your data in -- and without the compress parameter-- ie, something like: > setwd("/home/bioinfo/RatDiet") > data <- read.exon() > .. etc. Crispin On 24/4/08 08:19, "Rob Dunne" <rob.dunne at="" csiro.au=""> wrote: > > Hello Bioconductor list, > > I get an error when I try to rma normalize a data set of > Rat Exon 1.0 ST cel files i.e. > > library(exonmap) > library(ratexonpmcdf) # Rat Exon 1.0ST from > #http://xmap.picr.man.ac.uk/download/ > > data<-read.exon(path="/home/bioinfo/RatDiet/",compress=TRUE) > data at cdfName > #[1] "RaGene-1_0-st-v1" > data at cdfName <- "ratexonpmcdf" > X<-rma(data) > #Error in .local(object, ...) : subscript out of bounds > > length(probeNames(data)) #3999056 > length(data) #59 > length(geneNames(data)) #1018777 > > The problem occurs in the "pm" function where it appears that > an index is generated that is much larger than the matrix of > expression values. > > I have no problems with the human array tutorial example provided at > http://bioinformatics.picr.man.ac.uk/ > > > Bye > Rob > > _______________________________________________ > 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 -------------------------------------------------------- This email is confidential and intended solely for the u...{{dropped:12}}

ADD COMMENT • link 16.0 years ago Crispin Miller ★ 1.1k

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Hi Crespin, Crispin Miller wrote: > Hi Rob, > That's curious... > yes. It only happens with my data set. I just tried the Rat exon data set from the Affymetrix site with no problems. > Please can you let us know which versions of the software you're running > with a call to: > > >> sessionInfo() >> > sessionInfo() R version 2.6.2 (2008-02-08) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_AU.UTF-8;LC_NUMERIC=C;LC_TIME=en_AU.UTF-8;LC_COLLATE=en_AU .UTF-8; LC_MONETARY=en_AU.UTF-8;LC_MESSAGES=en_AU.UTF-8; LC_PAPER=en_AU.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C; LC_MEASUREMENT=en_AU.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] ratexonpmcdf_1.1 exonmap_1.4.3 plier_1.8.0 [4] RMySQL_0.6-0 DBI_0.2-4 RColorBrewer_1.0-2 [7] simpleaffy_2.14.05 gcrma_2.10.0 matchprobes_1.10.0 [10] genefilter_1.16.0 survival_2.34-1 affy_1.16.0 [13] preprocessCore_1.0.0 affyio_1.6.1 Biobase_1.16.3 loaded via a namespace (and not attached): [1] annotate_1.16.1 AnnotationDbi_1.0.6 RSQLite_0.6-8 > > > -- and what platform (i.e. Linux, Windows, Mac OS X ...) you're running on. > Linux, an AMD Opteron machine > Do you get the same error if you call read.exon() from the directory with > your data in -- and without the compress parameter-- ie, something like: > > >> setwd("/home/bioinfo/RatDiet") >> data <- read.exon() >> .. etc. >> yes -- its just the same. If it is the data, are there any consistency checks I can do? I can extract the probe values with no problem X<-exprs(data) > dim(X) [1] 1102500 59 > anyis.na(X)) [1] FALSE Bye Rob -- Rob Dunne Fax: +61 2 9325 3200 Tel: +61 2 9325 3263 CSIRO Mathematical and Information Sciences +61 2 9325 3100 Locked Bag 17, North Ryde, New South Wales, Australia, 1670 http://www.bioinformatics.csiro.au Email: Rob.Dunne at csiro.au Java has certainly revolutionized marketing and litigation.

ADD REPLY • link 16.0 years ago Rob Dunne ▴ 230

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Hi, On 28/4/08 11:24, "Rob Dunne" <rob.dunne at="" csiro.au=""> wrote: > Hi Crespin, > > Crispin Miller wrote: >> Hi Rob, >> That's curious... >> > yes. It only happens with my data set. I just tried the Rat exon data > set from the > Affymetrix site with no problems. > Are the CEL files the same size? Do they have the same cdfNames? Crispin -------------------------------------------------------- This email is confidential and intended solely for the u...{{dropped:12}}

ADD REPLY • link 16.0 years ago Crispin Miller ★ 1.1k

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