[BioC] affy( ) error with mas5()

James W. MacDonald jmacdon at uw.edu
Fri Apr 25 19:43:01 CEST 2014 

Hi Ying,

Yes, it has to do with long vectors in R. For RMA you don't generate a 
long vector, but instead pass in a matrix to the C code (which will be 
converted to a vector, but R doesn't know about that as far as I can tell).

If you really care about using mas5(), you could install R-2.15.1 and 
its version of bioconductor and run mas5. The code for that function 
hasn't changed for years now (like since 2005), so it will do the same 
thing with R-2.15.1 that it would do with R-3.1.0.

Best,

Jim


On 4/25/2014 9:31 AM, ying chen wrote:
> Hi guys,
>
> Thanks a lot for the help and sorry for getting back to you so late :(.
>
> Now I got confused. Does it mean affy() cannot do a MAS5 of 3869 
> HG-U133_Plus_2 arrays with affy CDF because of the setting of R long 
> vectors, or I did something wrong? I did a RMA with no problem.
>
> Thanks,
>
> Ying
>
> > Date: Wed, 9 Apr 2014 10:58:44 -0400
> > From: jmacdon at uw.edu
> > To: mtmorgan at fhcrc.org
> > CC: bioconductor at r-project.org
> > Subject: Re: [BioC] affy( ) error with mas5()
> >
> > Hi Martin,
> >
> > > length(unlist(as.list(hgu133plus2cdf)))*3800
> > [1] 4592360800
> > > 2^31
> > [1] 2147483648
> >
> > So allintensities is definitely longer than 2^31-1
> >
> > Best,
> >
> > Jim
> >
> >
> >
> > On Wednesday, April 09, 2014 10:51:43 AM, Martin Morgan wrote:
> > > On 04/09/2014 07:44 AM, James W. MacDonald wrote:
> > >> Hi Ying,
> > >>
> > >>
> > >> On 4/9/2014 10:21 AM, Ying Chen wrote:
> > >>> Hi guys,
> > >>>
> > >>> I use affy to process over 3800 affy U133Plus2 arrays. rma() went
> > >>> well, but
> > >>> mas5() gave me the error during background correcting:
> > >>>
> > >>> Error in matrix(.C("affy_background_adjust_R",
> > >>> as.double(as.vector(allintensities)), :
> > >>> long vectors (argument 1) are not supported in .Fortran
> > >>>
> > >>> I have been using affy() for a long time and this is the first time
> > >>> I run into
> > >>> such error. Any suggestion?
> > >>
> > >> In R-3.0.0 support for long vectors was implemented. The NEWS file
> > >> for that
> > >> release says
> > >>
> > >> *
> > >>
> > >> Many calls to |.C()| have been replaced by |.Call()| to allow long
> > >> vectors to be supported (now or in the future). Regrettably several
> > >> packages had copied the non-API |.C()| calls and so failed.
> > >>
> > >> *
> > >>
> > >> |.C()| and |.Fortran()| do not accept long vector inputs. This is a
> > >> precaution as it is very unlikely that existing code will have been
> > >> written to handle long vectors (and the *R* wrappers often assume
> > >> that |length(x)| is an integer).
> > >>
> > >>
> > >> So it appears we need to convert the .C() call in bg.correct.mas to a
> > >> .Call() to
> > >> accommodate these changes. I sort of doubt this will happen before
> > >> the impending
> > >> release, unfortunately.
> > >
> > > To me this implies that length(allintensities) is greater than 2^31-1,
> > > or that it has gone through some intermediate stage that was larger
> > > than this. But that doesn't seem correct?
> > >
> > > If there's an easy way to reproduce this error then I'm happy to
> > > investigate...
> > >
> > > Martin
> > >
> > >>
> > >> Best,
> > >>
> > >> Jim
> > >>
> > >>
> > >>>
> > >>> Thanks a lot for the help!
> > >>>
> > >>> Ying
> > >>>
> > >>>> data <- ReadAffy()
> > >>>> eset <- mas5(data)
> > >>> background correction: mas
> > >>> PM/MM correction : mas
> > >>> expression values: mas
> > >>> background correcting...
> > >>> Error in matrix(.C("affy_background_adjust_R",
> > >>> as.double(as.vector(allintensities)), :
> > >>> long vectors (argument 1) are not supported in .Fortran
> > >>>> str(eset)
> > >>> Error in str(eset) : object 'eset' not found
> > >>>> sessionInfo()
> > >>> R version 3.0.2 (2013-09-25)
> > >>> Platform: x86_64-unknown-linux-gnu (64-bit)
> > >>>
> > >>> locale:
> > >>> [1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US
> > >>> [4] LC_COLLATE=en_US LC_MONETARY=en_US LC_MESSAGES=en_US
> > >>> [7] LC_PAPER=en_US LC_NAME=C LC_ADDRESS=C
> > >>> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C
> > >>>
> > >>> attached base packages:
> > >>> [1] parallel stats graphics grDevices utils datasets methods
> > >>> [8] base
> > >>>
> > >>> other attached packages:
> > >>> [1] hgu133plus2cdf_2.13.0 AnnotationDbi_1.24.0 affy_1.40.0
> > >>> [4] Biobase_2.22.0 BiocGenerics_0.8.0
> > >>>
> > >>> loaded via a namespace (and not attached):
> > >>> [1] affyio_1.30.0 BiocInstaller_1.12.0 DBI_0.2-7
> > >>> [4] IRanges_1.20.7 preprocessCore_1.24.0 RSQLite_0.11.4
> > >>> [7] stats4_3.0.2 tools_3.0.2 zlibbioc_1.8.0
> > >>> -----Original Message-----
> > >>> From: bioconductor-bounces at r-project.org
> > >>> [mailto:bioconductor-bounces at r-project.org] On Behalf Of Abugri 
> James
> > >>> Sent: Wednesday, April 09, 2014 4:35 AM
> > >>> To: bioconductor at r-project.org
> > >>> Subject: [BioC] rehh package for iHS and Rsb
> > >>>
> > >>> Dear Bioconductor community,
> > >>> I have expressly read the manual and done the tutorial for the rehh
> > >>> package a
> > >>> dozen times, but still unable to apply it to my P. falciparum SNP
> > >>> data set. I
> > >>> have the SNP.INFO for P. falciparum. AND r scripts to call the
> > >>> genotypes and
> > >>> haplotypes. Has anybody got an experience in implementing this 
> package.
> > >>>
> > >>> --
> > >>> *ABUGRI, James*
> > >>> *Lecturer*
> > >>> *Department of Applied Chemistry and Biochemistry* *Faculty of 
> Applied
> > >>> Sciences* *University For Development Studies, Navrongo Campus*
> > >>> *Mobile;
> > >>> +233244994359 or +233204088294*
> > >>>
> > >>> --
> > >>> * "The information contained in this email and any attachments may
> > >>> be legally
> > >>> privileged and confidential. If you are not an intended recipient,
> > >>> you are
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> > >>>
> > >>> [[alternative HTML version deleted]]
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> > >>> _______________________________________________
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> > >
> >
> > --
> > James W. MacDonald, M.S.
> > Biostatistician
> > University of Washington
> > Environmental and Occupational Health Sciences
> > 4225 Roosevelt Way NE, # 100
> > Seattle WA 98105-6099
> >
> > _______________________________________________
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> http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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