[BioC] Memory problem with rma()

[Damian Plichta [guest]]

Hi,

I am running rma() to correct, normalize and summarize a batch of ca. 5500 arrays. I have currently a memory limit of 8gb and the procedures exceeds that. I am guessing that it breaks at the background correction step. I investigated the temporary directory and it's only file called tmp_310151_rbg.root that was modified (size of that file is 16gb).  I attached the code below.

I tried the latest ROOT version and the one recommended at bioconductor (root_v5.34.14,root_v5.34.05). 

Any idea why is there the memory issue?

scheme.HuEx <- import.exon.scheme(
		filename = "Scheme_HuEx-1_0v2r2_hg19",
		layoutfile = "affyHuExome_design/HuEx-1_0-st-v2.r2.clf",
		schemefile = "affyHuExome_design/HuEx-1_0-st-v2.r2.pgf",
		probeset = "affyHuExome_design/HuEx-1_0-st-v2.na33.1.hg19.probeset.csv",
		transcript = "affyHuExome_design/HuEx-1_0-st-v2.na33.1.hg19.transcript.csv")

scheme.HuEx <- root.scheme("Scheme_HuEx-1_0v2r2_hg19.root")

data.HuEx <- import.data(
		scheme.HuEx,
		filename = "fhsCEL",
		filedir = "normalizationXPS/",
		celdir = "expression_CEL_raw/"
		)

data.HuEx <- root.data(scheme.HuEx, rootfile="fhsCEL_cel.root") 		
		
rma.HuEx.transcript <- rma(data.HuEx, filename="HuEx_RMAquantile", 
		filedir="normalizationXPS",
		tmpdir = "normalizationXPS/tmpDir", 
		add.data=FALSE, background="antigenomic", normalize=TRUE,
		option="transcript", exonlevel="core")


 -- output of sessionInfo(): 

R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

other attached packages:
[1] xps_1.22.2

loaded via a namespace (and not attached):
[1] tools_3.0.2

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