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@uw.edu
> To: mtmorgan@fhcrc.org
> CC: bioconductor@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     Many calls to |.C()| have been replaced by |.Call()| to allow long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@r-project.org
> >>> [mailto:bioconductor-bounces@r-project.org] On Behalf Of Abugri James
> >>> Sent: Wednesday, April 09, 2014 4:35 AM
> >>> To: bioconductor@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
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> >>>
> >>>     [[alternative HTML version deleted]]
> >>>
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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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