[BioC] Memory problem with rma()

[plichta at cbs.dtu.dk]

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 at 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 at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>