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

[cstrato]

Dear Susan,

Please note that package "xps" was created to handle this amount of data 
on computers with 1-2GB RAM only, especially on WinXP.
However, only the verbose output can tell me what the problem might be.

Christian


On 8/27/10 7:33 PM, Susan R. Atlas wrote:
> 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
>>
>>
>>
>>
>>
>>
>
>
>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor