How much RAM do you have on your machine?  It looks like it is running
out...

Unfortunately the current approach to solving this problem (both in minfi
and methylumi) is "buy more RAM"....  :-(



On Fri, Dec 9, 2011 at 6:50 AM, Magdalena Wozniak <
wozniak.magdalena@gmail.com> wrote:

> Hi,
>
> I must admit I'm quite new to both methylation data analysis and R. I am
> currently analyzing IlluminaHumanMethylation450k data starting from IDAT
> files.
> The command:
>
> > barcodes <- c('6055432006_R04C01',+ '6055432006_R04C01',+ '6042316163_R06C02',+
> '6042316163_R06C02',...{other barcodes omitted})
>
> works well when I upload only few samples but gives the following error
> when I am trying to upload all the samples I want to analyse:
>
> > lumi450k <- methylumIDAT (barcodes)Warning: filtering out duplicate
> barcodes0 HumanMethylation27 samples found294 HumanMethylation450 samples
> foundError in annotation(NChannelSet) :
>  error in evaluating the argument 'object' in selecting a method for
> function 'annotation': Error: cannot allocate vector of size 8.0 Mb
>
> How could I increase the size allocated to a vector?
>
> When I submit only 2 samples the initial code works well and I get the
> MethylumiSetObject, however, I don't know how to change beta values to
> m-values, and MethyLumiSet to MethyLumiM object as when I want to do
> color balance adjustment, I obtain the following error:
>
>
> > lumiMethy.c.adj <- lumiMethyC(lumi450k)Error in lumiMethyC(lumi450k) :
>  The object should be class "MethyLumiM" inherited!
>
>
> I would be very grateful for help. I attach session info below:
>
> > sessionInfo()R version 2.14.0 (2011-10-31)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United
> Kingdom.1252
> [3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] IlluminaHumanMethylation450k.db_1.4.6 org.Hs.eg.db_2.6.4
>  [3] RSQLite_0.11.1                        DBI_0.2-5
>  [5] AnnotationDbi_1.16.9                  matrixStats_0.4.2
>  [7] R.methodsS3_1.2.1                     limma_3.10.0
>  [9] lumi_2.6.0                            nleqslv_1.9.1
> [11] methylumi_2.0.1                       Biobase_2.14.0
>
> loaded via a namespace (and not attached):
>  [1] affy_1.32.0           affyio_1.22.0         annotate_1.32.0
> BiocInstaller_1.2.1
>  [5] grid_2.14.0           hdrcde_2.15           IRanges_1.12.4
> KernSmooth_2.23-7
>  [9] lattice_0.20-0        MASS_7.3-16           Matrix_1.0-2
> mgcv_1.7-11
> [13] nlme_3.1-102          preprocessCore_1.16.0 tools_2.14.0
> xtable_1.6-0
> [17] zlibbioc_1.0.0
>
>
> >
>
>
> Best wishes,
> Magdalena
>
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>
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-- 
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/~history/Biographies/Von_Neumann.html>

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