[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.
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
--
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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