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

[cstrato]

Dear Mike,

In case that your problem turns out to be a memory-related problem, you 
can use rma(...,add.data=FALSE,..), which will prevent filling slot 
"data" with the expression levels. You can then import all normalized 
data or parts thereof using "export.expr()" or "root.expr()", as the 
help files show.

Thus you could first run rma and then import the results in a separate step:

## rma
 > data.rma <- rma(data.xps, "tmpdt_dataRMA", background="antigenomic", 
normalize=T, exonlevel=exonlevel,  add.data=FALSE, verbose = TRUE)

## import subset of trees:
ds <- export.expr(data.rma, treenames=c("name1.mdp","name3.mdp", etc), 
treetype="mdp", varlist="fUnitName:fSymbol:fLevel", outfile="tmp.txt", 
as.dataframe=TRUE)

## use subset of trees
 > sub.rma <- root.expr(scheme.test3, "tmpdt_dataRMA.root", "mdp", 
c("name1.mdp", "name2", etc))
 > str(sub.rma)

Maybe after starting a new R-session, you are able to import all trees 
with "treenames='*'".

Please let me know if this could solve your problem.

Best regards
Christian


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.
>
> 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
>
>
>
>
>