Hi Damian,

Soon, Christian should reply to you.

In the meantime, for my personal interest and to define plans for the oligo
package, would you be willing to try processing your set with oligo?

library(ff)
library(oligo)
cels = list.celfiles()
raw = read.celfiles(cels)
res = rma(raw)

If you have multiple cores available, before loading oligo, load a parallel
front-end:

library(doMC)
registerDoMC(4)

Let me know how it goes, if you have some time to spare...

Thanks a million, benilton
On Feb 16, 2014 7:15 PM, <plichta@cbs.dtu.dk> wrote:

> I don't get a proper error message because I'm running the R session in an
> interactive shell on a cluster (queuing system). When the memory limit of
> 8gb is reached, my interactive shell is terminated by the queuing system.
>
> > And what was the actual error that you got?
> >
> > Sean
> >
> >
> >
> > On Sun, Feb 16, 2014 at 2:07 PM, Damian Plichta [guest] <
> > guest@bioconductor.org> wrote:
> >
> >>
> >> Hi,
> >>
> >> I am running rma() to correct, normalize and summarize a batch of ca.
> >> 5500
> >> arrays. I have currently a memory limit of 8gb and the procedures
> >> exceeds
> >> that. I am guessing that it breaks at the background correction step. I
> >> investigated the temporary directory and it's only file called
> >> tmp_310151_rbg.root that was modified (size of that file is 16gb).  I
> >> attached the code below.
> >>
> >> I tried the latest ROOT version and the one recommended at bioconductor
> >> (root_v5.34.14,root_v5.34.05).
> >>
> >> Any idea why is there the memory issue?
> >>
> >> scheme.HuEx <- import.exon.scheme(
> >>                 filename = "Scheme_HuEx-1_0v2r2_hg19",
> >>                 layoutfile = "affyHuExome_design/HuEx-1_0-st-v2.r2.clf",
> >>                 schemefile = "affyHuExome_design/HuEx-1_0-st-v2.r2.pgf",
> >>                 probeset =
> >> "affyHuExome_design/HuEx-1_0-st-v2.na33.1.hg19.probeset.csv",
> >>                 transcript =
> >> "affyHuExome_design/HuEx-1_0-st-v2.na33.1.hg19.transcript.csv")
> >>
> >> scheme.HuEx <- root.scheme("Scheme_HuEx-1_0v2r2_hg19.root")
> >>
> >> data.HuEx <- import.data(
> >>                 scheme.HuEx,
> >>                 filename = "fhsCEL",
> >>                 filedir = "normalizationXPS/",
> >>                 celdir = "expression_CEL_raw/"
> >>                 )
> >>
> >> data.HuEx <- root.data(scheme.HuEx, rootfile="fhsCEL_cel.root")
> >>
> >> rma.HuEx.transcript <- rma(data.HuEx, filename="HuEx_RMAquantile",
> >>                 filedir="normalizationXPS",
> >>                 tmpdir = "normalizationXPS/tmpDir",
> >>                 add.data=FALSE, background="antigenomic",
> >> normalize=TRUE,
> >>                 option="transcript", exonlevel="core")
> >>
> >>
> >>  -- output of sessionInfo():
> >>
> >> R version 3.0.2 (2013-09-25)
> >> Platform: x86_64-unknown-linux-gnu (64-bit)
> >>
> >> locale:
> >>  [1] LC_CTYPE=C                 LC_NUMERIC=C
> >>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> >>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
> >>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
> >>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> >>
> >> attached base packages:
> >> [1] stats     graphics  grDevices utils     datasets  methods   base
> >>
> >> other attached packages:
> >> [1] xps_1.22.2
> >>
> >> loaded via a namespace (and not attached):
> >> [1] tools_3.0.2
> >>
> >> --
> >> Sent via the guest posting facility at bioconductor.org.
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >
>
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