R: R: R: R: Probe-level analysis of exon arrays using xps
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cstrato ★ 3.9k
@cstrato-908
Last seen 5.6 years ago
Austria
Dear Giovanni, I have just received your mail exactly one minute after sending you the explanation for the crash. From your newest mail it is clear why you cannot import the expression table, since you are using option="probeset" which increases the size of the table even further. So to prevent the crash you need to use: > data.rma <- rma(data.exon, ..., add.data=FALSE) Best regards Christian On 9/12/11 9:07 PM, Lavorgna Giovanni wrote: > Dear Christian, > > thanks for your answer. Sorry for not being clear in my previous massage. I'll try to clarify things a little bit more. > The following script running in a R session ( xps_1.12.1 + root 5.27/04) crashes after finishing the rma step, i.e., it completes the line: > > rma.ps.core<- rma(data.mix.exon, "MixExonRMAcorePS_prostate_CPU2", filedir=libdir, tmpdir="", background="antigenomic", normalize=TRUE, option="probeset", exonlevel="affx+core") > > producing both the correct root and text files, then hangs and gets killed by the system after memory consumption gets over 90%. > > > =========================================== > R script > snip > > =============================================== >> sessionInfo() > R version 2.13.1 (2011-07-08) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US > [4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=en_US > [7] LC_PAPER=en_US LC_NAME=C LC_ADDRESS=C > [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] xps_1.12.1 > > > ----------------------------------------------------------- > Giovanni Lavorgna > DIBIT-HSR > Via Olgettina, 58 > 20132 Milan Italy > Tel: +39-02-2643-4776 > Fax: +39-02-2643-4767 > Email: giovanni.lavorgna at hsr.it > >> >
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@lavorgna-giovanni-4817
Last seen 5.3 years ago
Dear Christian, many thanks for your further advice on this matter. Next few days, I will try your workarounds and I'll let you know how things go. Once again, thanks for your support even late at nights :-) Giovanni ----------------------------------------------------------- Giovanni Lavorgna DIBIT-HSR Via Olgettina, 58 20132 Milan Italy Tel: +39-02-2643-4776 Fax: +39-02-2643-4767 Email: giovanni.lavorgna at hsr.it ________________________________________ Da: cstrato [cstrato at aon.at] Inviato: luned? 12 settembre 2011 21.36 A: Lavorgna Giovanni Cc: bioconductor at r-project.org Oggetto: Re: R: R: R: R: [BioC] Probe-level analysis of exon arrays using xps Dear Giovanni, I have just received your mail exactly one minute after sending you the explanation for the crash. From your newest mail it is clear why you cannot import the expression table, since you are using option="probeset" which increases the size of the table even further. So to prevent the crash you need to use: > data.rma <- rma(data.exon, ..., add.data=FALSE) Best regards Christian On 9/12/11 9:07 PM, Lavorgna Giovanni wrote: > Dear Christian, > > thanks for your answer. Sorry for not being clear in my previous massage. I'll try to clarify things a little bit more. > The following script running in a R session ( xps_1.12.1 + root 5.27/04) crashes after finishing the rma step, i.e., it completes the line: > > rma.ps.core<- rma(data.mix.exon, "MixExonRMAcorePS_prostate_CPU2", filedir=libdir, tmpdir="", background="antigenomic", normalize=TRUE, option="probeset", exonlevel="affx+core") > > producing both the correct root and text files, then hangs and gets killed by the system after memory consumption gets over 90%. > > > =========================================== > R script > snip > > =============================================== >> sessionInfo() > R version 2.13.1 (2011-07-08) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US > [4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=en_US > [7] LC_PAPER=en_US LC_NAME=C LC_ADDRESS=C > [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] xps_1.12.1 > > > ----------------------------------------------------------- > Giovanni Lavorgna > DIBIT-HSR > Via Olgettina, 58 > 20132 Milan Italy > Tel: +39-02-2643-4776 > Fax: +39-02-2643-4767 > Email: giovanni.lavorgna at hsr.it > >> >
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