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

[cstrato]

Dear Mike,

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 
this correct?

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?

Best regards
Christian
_._._._._._._._._._._._._._._._._._
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
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.
>
> 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
>
>
>
>
>