[BioC] Reading methylation data using lumi package

[Yue Yu]

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 at gmail.com [mailto:seandavi at 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!
>
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