[BioC] affy( ) error with mas5()

[Ying Chen]

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?

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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