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

[James Carman]

Looks like that worked for me (after it downloaded hgu95av2cdf of
course).  So, what does that mean?

On Fri, Jan 28, 2011 at 11:40 AM, James W. MacDonald
<jmacdon at med.umich.edu> wrote:
> 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
>>
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>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
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> 734-615-7826
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