[BioC] affy( ) error with mas5()
James W. MacDonald
jmacdon at uw.edu
Wed Apr 9 16:58:44 CEST 2014
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 Many calls to |.C()| have been replaced by |.Call()| to allow long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*
>>>
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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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