[BioC] Can't normalize 300+ HuGene arrays in xps
cstrato at aon.at
Fri Aug 27 17:08:38 CEST 2010
At the moment I do not see any problem with your code. Since you mention
that you have successfully used xps with 180 samples and 144 samples,
respectively, I assume that you have used the same code as earlier, is
If not, then could you try to run the code on RTerm with a subset of 6
samples only and show me the verbose output.
You can do:
> celnames <- c("name1", "name2", etc) #the names of 6 of your cel files
> data.xps <- root.data(gene.scheme,
paste(getwd(),"Genepi_all_cel.root",sep="/"), celnames =celnames)
> data.rma <- rma(data.xps, "tmpdt_dataRMA", background="antigenomic",
normalize=T, exonlevel=exonlevel, verbose = TRUE)
If this works, then could you try to repeat your run on RTerm with
verbose=TRUE and send me the complete output (at least the part that you
are able to copy):
> data.norm = normalize.quantiles(data.bkgd, filename = "quantile",
filedir = getwd(),
tmpdir = "", update = FALSE, exonlevel =
exonlevel, verbose = TRUE)
Please note that it is important for me to see the complete verbose
output, since often only this output could show me where the problem is.
Some more questions:
Did you run R as RGui or from the console as RTerm?
Are you sure that you have enough hard disk space since
normalize.quantiles() will use a lot of disk space?
e.m.a.i.l: cstrato at aon.at
On 8/27/10 3:35 PM, Mike Walter wrote:
> 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.
> R version 2.10.1 (2009-12-14)
>  LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252
>  LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
>  LC_TIME=German_Germany.1252
> attached base packages:
>  stats graphics grDevices utils datasets methods base
> other attached packages:
>  xps_1.6.4
> loaded via a namespace (and not attached):
>  tools_2.10.1
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