Hi,
  Try a 64-bit machine.
   - Susan

------------------------------------------------------------------------

> 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.
>
> library(xps)
> memory.limit(size=3000) # I modyfied my boot.ini to allow more memory. At least I hope it works.
> exonlevel=rep((8192+1024),3)
> scheme="Scheme_HuGene10stv1r4_na30_hg19.root"
> 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)
>
> OR
>
>
> 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.
>
> Best,
> Mike
>
>   
>> sessionInfo()
>>     
> R version 2.10.1 (2009-12-14) 
> i386-pc-mingw32 
>
> locale:
> [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
>
>
>
>
>
>   


-- 
------------------------------------------------------------------
 Susan R. Atlas
 Research Associate Professor, Physics and Astronomy
 Director, Center for Advanced Research Computing
 Director, University of New Mexico Cancer Center Shared Resource
    for Bioinformatics and Computational Biology

 Department of Physics & Astronomy
 MSC07 4220                       p: 505.277.1509
 1 University of New Mexico       e: susie@sapphire.phys.unm.edu
 Albuquerque, NM 87131-0001       n: www.phys.unm.edu/CompMaterials


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