[BioC] segfault ReadAffy cause 'memory not mapped'
Matthew McCall
mccallm at gmail.com
Fri Aug 2 23:57:04 CEST 2013
Another option if your data comes from one of the more common
affymetrix platforms (HGU133a, HGU133plus2, Mouse4302, HuGene, HuEx),
you can read in and preprocess your data in subsets using frma and
then combine it for further analysis.
Best,
Matt
On Fri, Aug 2, 2013 at 4:59 PM, Adaikalavan Ramasamy
<adaikalavan.ramasamy at gmail.com> wrote:
> Also worth trying the standalone and free software called affy power tools
> if its affy arrays. There is an option to choose sketch normalization.
>
> On 2 Aug 2013 21:34, "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com>
> wrote:
>
>> ReadAffy constructs a matrix which is probes x samples. If the array is
>> big enough, perhaps several thousand samples is enough to push a matrix
>> over the internal R limits.
>>
>> Which array is this?
>>
>> Kasper
>>
>>
>> On Fri, Aug 2, 2013 at 4:17 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
>>
>> > On 08/02/2013 11:00 AM, cstrato wrote:
>> >
>> >> Dear Ann,
>> >>
>> >> Several thousand CEL-files is quite a lot. Furthermore, you do not
>> >> mention which
>> >> array type are you using.
>> >>
>> >> In any case you could try to use package 'xps', which should be able to
>> >> handle
>> >> it. However, you should do your processing stepwise.
>> >>
>> >
>> > also, perhaps justRMA is a more memory-efficient way to do standard
>> > normalization. Probably there is a bug in ReadAffy, but it would be
>> > difficult to track down without a more reproducible example. Martin
>> >
>> >
>> >
>> >> 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 8/1/13 5:33 PM, Loraine, Ann wrote:
>> >>
>> >>> Hello,
>> >>>
>> >>> I am trying to process several thousand CEL files using the ReadAffy
>> >>> command.
>> >>>
>> >>> The machine has 96 Gb RAM.
>> >>>
>> >>> However I get this error:
>> >>>
>> >>> expr=ReadAffy(filenames=d.**uniq$cel,celfile.path='CEL',**
>> >>>> sampleNames=d.uniq$gsm,**compress=T)
>> >>>>
>> >>>>
>> >>> *** caught segfault ***
>> >>> address 0x7fc79b4b1048, cause 'memory not mapped'
>> >>>
>> >>> Traceback:
>> >>> 1: .Call("read_abatch", filenames, rm.mask, rm.outliers, rm.extra,
>> >>> ref.cdfName, dim.intensity[c(1, 2)], verbose, PACKAGE = "affyio")
>> >>> 2: read.affybatch(filenames = l$filenames, phenoData = l$phenoData,
>> >>> description = l$description, notes = notes, compress = compress,
>> >>> rm.mask =
>> >>> rm.mask, rm.outliers = rm.outliers, rm.extra = rm.extra, verbose =
>> >>> verbose, sd = sd, cdfname = cdfname)
>> >>> 3: ReadAffy(filenames = d.uniq$cel, celfile.path = "CEL",
>> sampleNames =
>> >>> d.uniq$gsm, compress = T)
>> >>>
>> >>> Possible actions:
>> >>> 1: abort (with core dump, if enabled)
>> >>> 2: normal R exit
>> >>> 3: exit R without saving workspace
>> >>> 4: exit R saving workspace
>> >>> Selection:
>> >>>
>> >>> R and session info:
>> >>>
>> >>> R version 3.0.1 (2013-05-16) -- "Good Sport"
>> >>> Copyright (C) 2013 The R Foundation for Statistical Computing
>> >>> Platform: x86_64-unknown-linux-gnu (64-bit)
>> >>>
>> >>> sessionInfo()
>> >>>>
>> >>> R version 3.0.1 (2013-05-16)
>> >>> Platform: x86_64-unknown-linux-gnu (64-bit)
>> >>>
>> >>> locale:
>> >>> [1] LC_CTYPE=en_US.UTF-8 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=C LC_NAME=C
>> >>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> >>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>> >>>
>> >>> attached base packages:
>> >>> [1] parallel stats graphics grDevices utils datasets methods
>> >>> [8] base
>> >>>
>> >>> other attached packages:
>> >>> [1] affy_1.38.1 Biobase_2.20.1 BiocGenerics_0.6.0
>> >>>
>> >>> loaded via a namespace (and not attached):
>> >>> [1] affyio_1.28.0 BiocInstaller_1.10.3 preprocessCore_1.22.0
>> >>> [4] zlibbioc_1.6.0
>> >>>
>> >>> Can you help?
>> >>>
>> >>> Best,
>> >>>
>> >>> Ann
>> >>>
>> >>>
>> >>> [[alternative HTML version deleted]]
>> >>>
>> >>> ______________________________**_________________
>> >>> Bioconductor mailing list
>> >>> Bioconductor at r-project.org
>> >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<
>> https://stat.ethz.ch/mailman/listinfo/bioconductor>
>> >>> Search the archives:
>> >>> http://news.gmane.org/gmane.**science.biology.informatics.**conductor<
>> http://news.gmane.org/gmane.science.biology.informatics.conductor>
>> >>>
>> >>>
>> >> ______________________________**_________________
>> >> Bioconductor mailing list
>> >> Bioconductor at r-project.org
>> >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<
>> https://stat.ethz.ch/mailman/listinfo/bioconductor>
>> >> Search the archives:
>> >> http://news.gmane.org/gmane.**science.biology.informatics.**conductor<
>> http://news.gmane.org/gmane.science.biology.informatics.conductor>
>> >>
>> >
>> >
>> > --
>> > Computational Biology / Fred Hutchinson Cancer Research Center
>> > 1100 Fairview Ave. N.
>> > PO Box 19024 Seattle, WA 98109
>> >
>> > Location: Arnold Building M1 B861
>> > Phone: (206) 667-2793
>> >
>> >
>> > ______________________________**_________________
>> > Bioconductor mailing list
>> > Bioconductor at r-project.org
>> > https://stat.ethz.ch/mailman/**listinfo/bioconductor<
>> https://stat.ethz.ch/mailman/listinfo/bioconductor>
>> > Search the archives: http://news.gmane.org/gmane.**
>> > science.biology.informatics.**conductor<
>> http://news.gmane.org/gmane.science.biology.informatics.conductor>
>> >
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> 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
>>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> 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
--
Matthew N McCall, PhD
112 Arvine Heights
Rochester, NY 14611
Cell: 202-222-5880
More information about the Bioconductor
mailing list