[BioC] IDAT files upload error, MethyLumiM object: IlluminaHumanMethylation450k

[Nicholas Wong]

Tim, do you have any metrics to the RAM issue?

eg: is it 450kb per array/sample for instance?

cheers



On 10/12/2011, at 7:21 AM, Tim Triche, Jr. wrote:

> 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 at 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
>> 
>>       [[alternative HTML version deleted]]
>> 
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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>
> 
> 	[[alternative HTML version deleted]]
> 
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