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
> >>
> >
> >
>

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