[BioC] Can't normalize 300+ HuGene arrays in xps

Mike Walter michael_walter at email.de
Fri Aug 27 15:35:39 CEST 2010

Hi all,

I have a set of 324 HuGene 1.0 arrays I'd like to normalize all in one batch on a "normal" Windows computer. I allready normalized the arrays in two sets of 180 and 144 samples successfully with xps. When I apply the code below to put the samples all together, my R session just crashes.

memory.limit(size=3000) # I modyfied my boot.ini to allow more memory. At least I hope it works.
gene.scheme <- root.scheme(paste("X:/affy/QC_Scripts/xps/schemes",scheme,sep="/"))
data.xps = root.data(gene.scheme, paste(getwd(),"Genepi_all_cel.root",sep="/"))
data.rma <- rma(data.xps, "tmpdt_dataRMA", background="antigenomic", normalize=T, 
                    exonlevel=exonlevel, verbose = FALSE)

Thus, I tried to do the RMA stepwise. I succeeded in background correction, but get some error when trying to do the quantile normalization:

data.bkgd = bgcorrect.rma(data.xps, filename = "bkgd_correct", 
                    filedir = getwd(), tmpdir = "", update = FALSE, 
                    select = "antigenomic", exonlevel = exonlevel, verbose = FALSE)

data.norm = normalize.quantiles(data.bkgd, filename = "quantile", filedir = getwd(), 
                     tmpdir = "", update = FALSE, exonlevel = exonlevel, verbose = FALSE)


data.norm = normalize(data.bkgd, "quantile", filedir=getwd(), tmpdir="", 
                    method="quantile", select="pmonly", option="transcript:together:none", 
                    logbase="0", params=c(0.0), exonlevel=exonlevel)

in both cases the output is "Fehler in .local(object, ...) : error in function ‘Normalize’". I guess it is only a wrong option somewhere. I also tried exonlevel="metacore+affx" with same result. Can anyone give me a hint, what might be missing?

Thank you very much.


> sessionInfo()
R version 2.10.1 (2009-12-14) 

[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252   
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C                   
[5] LC_TIME=German_Germany.1252    

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

other attached packages:
[1] xps_1.6.4

loaded via a namespace (and not attached):
[1] tools_2.10.1

Dr. Michael Walter
MFT Services
University of Tübingen
Calwerstr. 7
72076  Tübingen

Tel.: +49 7071 29 83210
Fax. + 49 7071 29 5228
web: www.mft-services.de

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