[BioC] affy( ) error with mas5()

[James W. MacDonald]

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    Many calls to |.C()| have been replaced by |.Call()| to allow long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.

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*
>
> --
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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