[BioC] Large datasets in methylumi

[Andrew Beggs [guest]]

Hi,

I am trying to analyse a large dataset in methylumi - 300 samples on HumanMethylation450 arrays. I get the following error message if I try and analyse the dataset whole:

lumi450 <- methylumIDAT(meth450barcodes,idatPath=getwd(),parallel=TRUE)

Error in annotation(NChannelSet) : 
  error in evaluating the argument 'object' in selecting a method for function 'annotation': Error in x[[assay]] : subscript out of bounds

If I split the dataset into three it works fine, but I'd rather run the analysis whole for simplicity.

I have 32gb of system RAM and looking at top it doesn't look like R is running out of memory.

Any suggestions?

 -- output of sessionInfo(): 

R version 2.15.2 (2012-10-26)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] methylumi_2.4.0    ggplot2_0.9.3      reshape2_1.2.2     scales_0.2.3      
[5] Biobase_2.18.0     BiocGenerics_0.4.0

loaded via a namespace (and not attached):
 [1] annotate_1.36.0      AnnotationDbi_1.20.3 colorspace_1.2-0    
 [4] DBI_0.2-5            dichromat_1.2-4      digest_0.6.0        
 [7] grid_2.15.2          gtable_0.1.2         IRanges_1.16.4      
[10] labeling_0.1         lattice_0.20-10      MASS_7.3-22         
[13] munsell_0.4          plyr_1.8             proto_0.3-9.2       
[16] RColorBrewer_1.0-5   RSQLite_0.11.2       stats4_2.15.2       
[19] stringr_0.6.2        tools_2.15.2         XML_3.95-0.1        
[22] xtable_1.7-0  

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