[BioC] segfault ReadAffy cause 'memory not mapped'
Henrik Bengtsson
hb at biostat.ucsf.edu
Sat Aug 3 00:06:30 CEST 2013
Alright, my turn...
http://aroma-project.org/
/Henrik
On Fri, Aug 2, 2013 at 2:57 PM, Matthew McCall <mccallm at gmail.com> wrote:
> 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]]
>>> >>>
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>
>
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> Matthew N McCall, PhD
> 112 Arvine Heights
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> Cell: 202-222-5880
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