Reading methylation data using lumi package

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Yue Yu ▴ 20

@yue-yu-4568

Last seen 10.6 years ago

Hi guys, I was running lumi package to analyze the methylation data, and I used the following scripts: setwd('C:/Documents and Settings/xxx/My Documents/Downloads/HumanSamples') library(lumi) library(IlluminaHumanMethylation27k.db) data0<- 'Sample Methylation Profile.txt' sample.lumiMethy <- lumiMethyR(data0, lib="IlluminaHumanMethylation27k.db") I can not read in the data. The error is shown below: Error in if (mm < 0.01) { : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : Reached total allocation of 1535Mb: see help(memory.size) 2: In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : Reached total allocation of 1535Mb: see help(memory.size) 3: In slot(value, what) <- slot(from, what) : Reached total allocation of 1535Mb: see help(memory.size) 4: In slot(value, what) <- slot(from, what) : Reached total allocation of 1535Mb: see help(memory.size) My sectionInfo is shown below: > sessionInfo() R version 2.12.2 (2011-02-25) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] IlluminaHumanMethylation27k.db_1.4.0 org.Hs.eg.db_2.4.6 RSQLite_0.9-4 DBI_0.2-5 [5] AnnotationDbi_1.12.0 lumi_2.2.1 Biobase_2.10.0 loaded via a namespace (and not attached): [1] affy_1.28.0 affyio_1.18.0 annotate_1.28.1 grid_2.12.2 hdrcde_2.15 KernSmooth_2.23-4 lattice_0.19-17 [8] MASS_7.3-11 Matrix_0.999375-46 methylumi_1.6.1 mgcv_1.7-3 nlme_3.1-98 preprocessCore_1.12.0 tools_2.12.2 [15] xtable_1.5-6 I am using windowsXP SP3 32bit, and my memory size is 3.16Gb. Any hint or suggestion will be much appreciated! Thanks a lot! [[alternative HTML version deleted]]

lumi lumi • 1.2k views

ADD COMMENT • link updated 14.0 years ago by Sean Davis 21k • written 14.0 years ago by Yue Yu ▴ 20

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Sean Davis 21k

@sean-davis-490

Last seen 7 weeks ago

United States

On Wed, Mar 30, 2011 at 1:39 PM, Yue Yu <yueyu at="" northwestern.edu=""> wrote: > Hi guys, > > I was running lumi package to analyze the methylation data, and I used the > following scripts: > > setwd('C:/Documents and Settings/xxx/My Documents/Downloads/HumanSamples') > library(lumi) > library(IlluminaHumanMethylation27k.db) > data0<- 'Sample Methylation Profile.txt' > sample.lumiMethy <- lumiMethyR(data0, lib="IlluminaHumanMethylation27k.db") > > I can not read in the data. The error is shown below: > > Error in if (mm < 0.01) { : missing value where TRUE/FALSE needed > In addition: Warning messages: > 1: In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, ?: > ?Reached total allocation of 1535Mb: see help(memory.size) > 2: In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, ?: > ?Reached total allocation of 1535Mb: see help(memory.size) > 3: In slot(value, what) <- slot(from, what) : > ?Reached total allocation of 1535Mb: see help(memory.size) > 4: In slot(value, what) <- slot(from, what) : > ?Reached total allocation of 1535Mb: see help(memory.size) It looks like probably need more memory. Sean > My sectionInfo is shown below: > >> sessionInfo() > R version 2.12.2 (2011-02-25) > Platform: i386-pc-mingw32/i386 (32-bit) > locale: > [1] LC_COLLATE=English_United States.1252 ?LC_CTYPE=English_United > States.1252 ? ?LC_MONETARY=English_United States.1252 > LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > other attached packages: > [1] IlluminaHumanMethylation27k.db_1.4.0 > org.Hs.eg.db_2.4.6 ? ? ? ? ? ? ? ? ? RSQLite_0.9-4 > DBI_0.2-5 > [5] AnnotationDbi_1.12.0 > lumi_2.2.1 ? ? ? ? ? ? ? ? ? ? ? ? ? Biobase_2.10.0 > loaded via a namespace (and not attached): > ?[1] affy_1.28.0 ? ? ? ? ? affyio_1.18.0 ? ? ? ? annotate_1.28.1 > grid_2.12.2 ? ? ? ? ? hdrcde_2.15 ? ? ? ? ? KernSmooth_2.23-4 > lattice_0.19-17 > ?[8] MASS_7.3-11 ? ? ? ? ? Matrix_0.999375-46 ? ?methylumi_1.6.1 > mgcv_1.7-3 ? ? ? ? ? ?nlme_3.1-98 ? ? ? ? ? preprocessCore_1.12.0 > tools_2.12.2 > [15] xtable_1.5-6 > > I am using windowsXP SP3 32bit, and my memory size is 3.16Gb. > > Any hint or suggestion will be much appreciated! Thanks a lot! > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

ADD COMMENT • link 14.0 years ago Sean Davis 21k

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Thank you so much for your input Sean! I will try a smaller data then. If it works, I will consider upgrading my system. -----Original Message----- From: seandavi@gmail.com [mailto:seandavi@gmail.com] On Behalf Of Sean Davis Sent: Wednesday, March 30, 2011 3:25 PM To: Yue Yu Cc: bioconductor at r-project.org Subject: Re: [BioC] Reading methylation data using lumi package On Wed, Mar 30, 2011 at 1:39 PM, Yue Yu <yueyu at="" northwestern.edu=""> wrote: > Hi guys, > > I was running lumi package to analyze the methylation data, and I used the > following scripts: > > setwd('C:/Documents and Settings/xxx/My Documents/Downloads/HumanSamples') > library(lumi) > library(IlluminaHumanMethylation27k.db) > data0<- 'Sample Methylation Profile.txt' > sample.lumiMethy <- lumiMethyR(data0, lib="IlluminaHumanMethylation27k.db") > > I can not read in the data. The error is shown below: > > Error in if (mm < 0.01) { : missing value where TRUE/FALSE needed > In addition: Warning messages: > 1: In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : > Reached total allocation of 1535Mb: see help(memory.size) > 2: In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : > Reached total allocation of 1535Mb: see help(memory.size) > 3: In slot(value, what) <- slot(from, what) : > Reached total allocation of 1535Mb: see help(memory.size) > 4: In slot(value, what) <- slot(from, what) : > Reached total allocation of 1535Mb: see help(memory.size) It looks like probably need more memory. Sean > My sectionInfo is shown below: > >> sessionInfo() > R version 2.12.2 (2011-02-25) > Platform: i386-pc-mingw32/i386 (32-bit) > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 LC_MONETARY=English_United States.1252 > LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] IlluminaHumanMethylation27k.db_1.4.0 > org.Hs.eg.db_2.4.6 RSQLite_0.9-4 > DBI_0.2-5 > [5] AnnotationDbi_1.12.0 > lumi_2.2.1 Biobase_2.10.0 > loaded via a namespace (and not attached): > [1] affy_1.28.0 affyio_1.18.0 annotate_1.28.1 > grid_2.12.2 hdrcde_2.15 KernSmooth_2.23-4 > lattice_0.19-17 > [8] MASS_7.3-11 Matrix_0.999375-46 methylumi_1.6.1 > mgcv_1.7-3 nlme_3.1-98 preprocessCore_1.12.0 > tools_2.12.2 > [15] xtable_1.5-6 > > I am using windowsXP SP3 32bit, and my memory size is 3.16Gb. > > Any hint or suggestion will be much appreciated! Thanks a lot! > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >

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