Memory error wihle processing 35 Affymetrix cel files

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Seth Falcon ★ 7.4k

@seth-falcon-992

Last seen 10.3 years ago

Gunther H?ning <gunther.hoening at="" ukmainz.de=""> writes: > Dear list, > > currently I'm trying to process 35 cel-files of the Affymetrix Human U133 > Plus 2.0 chip. > > I load the libraries and read the chips into an affybatch. > Background correction works well but during normalisation I always receive: > "Cannot allocate vector of size 352848...") > > I am using openlinux 10.2 with 2 GB RAM. > Does anyone know a solution to this problem ? > Using more RAM ? Yes. You can also look into justRMA, this might get you going. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org

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ADD COMMENT • link updated 17.8 years ago by Gunther Höning ▴ 100 • written 17.8 years ago by Seth Falcon ★ 7.4k

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Gunther Höning ▴ 100

@gunther-honing-1868

Last seen 10.3 years ago

Thanks for your suggestions, but I want to use my own summarization thus I only need the first two steps of array analysis. BG-correction and normalisation. data <- ReadAffy() eset <- bg.adjust.gcrma(data) eset.norm <- normalize(eset, method ="quantiles") .. and so on... So I can't use justRma or justgcrma. Thus more RAM. Thanks a lot... Gunther

ADD COMMENT • link 17.8 years ago Gunther Höning ▴ 100

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You can also do the obvious to delete objects/detach packages as soon as they are not needed anymore, .e.g. 'data' is not needed in the normalization step. Don't forget to call gc(). /Henrik On 3/27/07, H?ning, Gunther <gunther.hoening at="" ukmainz.de=""> wrote: > Thanks for your suggestions, > but I want to use my own summarization thus I only need the first two steps of array analysis. > BG-correction and normalisation. > > data <- ReadAffy() > eset <- bg.adjust.gcrma(data) > eset.norm <- normalize(eset, method ="quantiles") > .. and so on... > > So I can't use justRma or justgcrma. > Thus more RAM. > > Thanks a lot... > > Gunther > > _______________________________________________ > 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 >

ADD REPLY • link 17.8 years ago Henrik Bengtsson ★ 2.4k

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Dear list, as I mentioned in my task before (Memory error while processing 35 Affymetrix cel files) I analyze a lot of data. My own processing steps after bg-correction and normalization will (hopefully) improve the cel files I have. So I am looking for an suitable workstation configuration, e.g. 64bit architecture, 16 GB RAM.... etc. Does anyone have any experience with setting up such a system ? Gunther

ADD REPLY • link 17.8 years ago Gunther Höning ▴ 100

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On Wednesday 28 March 2007 08:28, Gunther H?ning wrote: > Dear list, > > as I mentioned in my task before (Memory error while processing 35 > Affymetrix cel files) I analyze a lot of data. My own processing steps > after bg-correction and normalization will (hopefully) improve the cel > files I have. > So I am looking for an suitable workstation configuration, e.g. 64bit > architecture, 16 GB RAM.... etc. > > Does anyone have any experience with setting up such a system ? You will want to run Linux or Unix of some kind. The hardware is pretty easy to find these days. Look for "workstations" at Dell, HP, etc. 64-bit, 16Gb of RAM used to require "setting up", but these days, these machines are relatively easy to come by for about $7000, most of which is memory costs. Sean

ADD REPLY • link 17.8 years ago Sean Davis 21k

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