sessioninfo() R version 2.13.0 (2011-04-13) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] lumi_2.4.0 nleqslv_1.8.3 Biobase_2.12.1 loaded via a namespace (and not attached): [1] affy_1.30.0 affyio_1.20.0 annotate_1.30.0 AnnotationDbi_1.14.1 DBI_0.2-5 grid_2.13.0 hdrcde_2.15 KernSmooth_2.23-4 [9] lattice_0.19-23 MASS_7.3-12 Matrix_0.999375-50 methylumi_1.8.0 mgcv_1.7-5 nlme_3.1-100 preprocessCore_1.14.0 RSQLite_0.9-4 [17] xtable_1.5-6 ls -l of that file : -rw-r--r-- 1 user staff 275681998 May 5 14:40 FinalReport_edit.txt Could it be that the file is too big to hold into memory? Is there a way to get around this ? Thanks a lot! On Thu, May 5, 2011 at 9:34 PM, Vincent Carey <stvjc@channing.harvard.edu>wrote: > you can still generate a sessionInfo() before getting into the bad > state. please do so; otherwise, we do not know what > software configuration is in play. furthermore, i would suggest using > the terminal to obtain results of "ls -l" on the files > that you imported. > > On Thu, May 5, 2011 at 10:05 PM, Jasreet <jovialj86@gmail.com> wrote: > > @ Sean: > > yes, It is Infinium HumanMethylation27 BeadChip > > > > @Vincent > > There is no error because all i see the mac - rainbow wheel.. And so I > end > > up 'force quiting' R without session info. > > > > > > On Thu, May 5, 2011 at 8:44 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > >> > >> > >> On Thu, May 5, 2011 at 9:04 PM, Vincent Carey < > stvjc@channing.harvard.edu> > >> wrote: > >>> > >>> Please read the posting guide. What is the error message? What is > >>> the result of sessionInfo()? > >>> > >>> On Thu, May 5, 2011 at 5:35 PM, Jasreet <jovialj86@gmail.com> wrote: > >>> > I am new to R and trying to analyze Illumina Infinium Array Data > using > >>> > 'lumi' package. > >>> > But whenever I try to load MethylumiM into annotation/color info > using > >>> > IlluminaHumanMethylation27k.db , its been crashing consistently! > >>> > Using R for MacOSX. > >>> > Command I used: > >>> > > >>> >>addColorChannelInfo <- lumiMethyR(myFile, > >>> > lib="IlluminaHumanMethylation27k.db") > >>> > > >>> > Here are the contents of the MethyLumiM object : > >>> >>myFile > >>> > MethyLumiM (storageMode: lockedEnvironment) > >>> > assayData: 485577 features, 12 samples > >> > >> And just to be clear, are you sure that you are using a 27k array? The > >> number of features looks to be something other than a 27k array? > >> Sean > >> > >>> > >>> > element names: detection, exprs, methylated, unmethylated > >>> > protocolData: none > >>> > phenoData > >>> > sampleNames: 3y0eY1 3y0eY2 ... 3y0eXY (12 total) > >>> > varLabels: sampleID label > >>> > varMetadata: labelDescription > >>> > featureData > >>> > featureNames: cg00000029 cg00000108 ... rs9839873 (485577 total) > >>> > fvarLabels: TargetID ProbeID_A ProbeID_B > >>> > fvarMetadata: labelDescription > >>> > experimentData: use 'experimentData(object)' > >>> > > >>> > Thanks! > >>> > J > >>> > > >>> > [[alternative HTML version deleted]] > >>> > > >>> > _______________________________________________ > >>> > Bioconductor mailing list > >>> > Bioconductor@r-project.org > >>> > https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> > Search the archives: > >>> > http://news.gmane.org/gmane.science.biology.informatics.conductor > >>> > > >>> > >>> _______________________________________________ > >>> Bioconductor mailing list > >>> Bioconductor@r-project.org > >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> Search the archives: > >>> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > > > > > [[alternative HTML version deleted]]

Tim, Thanks for the suggestion. I used addColorChannelInfo <- lumiMethyR(myFile,lib=" IlluminaHumanMethylation450k.db") and it did NOT crash! So it was indeed 450k data. Sorry, looks like there was a disconnect between the technicians in genotyping and us. Thanks to you, I have also updated them that we are dealing with 450k array!! :) Thanks for your time everyone. On Fri, May 6, 2011 at 10:49 AM, Tim Triche, Jr. <tim.triche@gmail.com>wrote: > On Thu, May 5, 2011 at 7:05 PM, Jasreet < <jovialj86@gmail.com> > jovialj86@gmail.com> wrote: > >> @ Sean: >> yes, It is Infinium HumanMethylation27 BeadChip >> > > OK, here's the part I don't understand. How do you end up with 485000+ > features and a 275MB file fromrr just 12 samples on 27k chips? The > information (and the presence of rsXXXXXX probes) strongly suggests that you > are dealing with 450k data. I'm not saying you are wrong, just that it's > very strange. What happens if you run > > addColorChannelInfo <- lumiMethyR(myFile, lib=" > IlluminaHumanMethylation450k.db") > > instead? Still crashing? > > > @Vincent >> There is no error because all i see the mac - rainbow wheel.. And so I end >> up 'force quiting' R without session info. >> > > Can you type > > library(lumi) > library(methylumi) > library(IlluminaHumanMethylation27k.db) > sessionInfo() > > and paste the result into an email? It might be possible for me to > reroduce your error with that information. > > Thanks! > > > -- > If people do not believe that mathematics is simple, it is only because > they do not realize how complicated life is. > John von Neumann<http: www-groups.dcs.st-="" and.ac.uk="" %7ehistory="" biographies="" von_neumann.html=""> > > [[alternative HTML version deleted]]