[BioC] Problem with affy mas5 on Linux but not Windows...

[James W. MacDonald]

Hi James,

On 1/28/2011 11:00 AM, James Carman wrote:
> If I try to run this code on Linux, it fails, but it works on Windows:
>
>> library(affy)
>> aff<- ReadAffy()
>> m5<- mas5(aff)
> background correction: mas
> PM/MM correction : mas
> expression values: mas
> background correcting...Error in as.vector(data) : NAs in foreign
> function call (arg 2)

Let's start with something simple. Can you run mas5() on the Dilution 
data from the affydata package? I get

 > library(affydata)
Loading required package: affy
Loading required package: Biobase

Welcome to Bioconductor

   Vignettes contain introductory material. To view, type
   'openVignette()'. To cite Bioconductor, see
   'citation("Biobase")' and for packages 'citation(pkgname)'.

 > data(Dilution)
 > m5 <- mas5(Dilution)
background correction: mas
PM/MM correction : mas
expression values: mas
background correcting...done.
12625 ids to be processed
|                    |
|####################|
 > sessionInfo()
R version 2.12.0 beta (2010-09-30 r53083)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
  [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
  [5] LC_MONETARY=C                  LC_MESSAGES=en_US.iso885915
  [7] LC_PAPER=en_US.iso885915       LC_NAME=C
  [9] LC_ADDRESS=C                   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] hgu95av2cdf_2.7.0 affydata_1.11.10  affy_1.28.0       Biobase_2.10.0

loaded via a namespace (and not attached):
[1] affyio_1.18.0         preprocessCore_1.12.0 tools_2.12.0

Best,

Jim


>
> Here's the result of sessionInfo():
>> sessionInfo()
> R version 2.12.1 (2010-12-16)
> Platform: x86_64-redhat-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
>   [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
>   [7] LC_PAPER=en_US.utf8       LC_NAME=C
>   [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] hgu133a2cdf_2.7.0 affy_1.28.0       Biobase_2.10.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.16.0         preprocessCore_1.10.0 tools_2.12.1
>
> Here's my platform:
>
>> uname -a
> Linux carman-op755 2.6.35.10-74.fc14.x86_64 #1 SMP Thu Dec 23 16:04:50
> UTC 2010 x86_64 x86_64 x86_64 GNU/Linux
>
> Here's the version of R that I'm running:
>
>> rpm -qa | grep R-
> R-core-2.12.1-1.fc14.x86_64
> R-devel-2.12.1-1.fc14.x86_64
> R-2.12.1-1.fc14.x86_64
>
>
> We have used this process in the past and it has worked fine.  I got a
> new computer and installed the latest Bioconductor package(s) on it
> and now I'm getting this failure.  Any ideas?
>
> Thank you,
>
> James Carman
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues