[BioC] affy( ) error with mas5()

[Martin Morgan]

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     Many calls to |.C()| have been replaced by |.Call()| to allow long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