[BioC] Problem with affy mas5 on Linux but not Windows...
James W. MacDonald
jmacdon at med.umich.edu
Fri Jan 28 18:41:36 CET 2011
On 1/28/2011 11:47 AM, James Carman wrote:
> Looks like that worked for me (after it downloaded hgu95av2cdf of
> course). So, what does that mean?
It means there isn't any weird Linux/mas5() interaction going on, so we
can look at your data. The error you report indicates you have some NA
values in your data somewhere. So the first step is to check.
any(is.na(exprs(aff)))
This should return TRUE. If so, you can track it down to the 'bad'
celfile by
apply(exprs(aff), 2, function(x) any(is.na(x)))
and then try re-uploading that celfile to your Linux box.
If not, you can try
debug(bg.correct.mas)
bg.correct.mas(aff)
and step through the function. The error comes at the line
corrected <- matrix(.C("affy_background_adjust_R",
as.double(as.vector(allintensities)),
as.integer(allx), as.integer(ally), as.integer(nprobes),
as.integer(nchips), as.integer(rows), as.integer(cols),
as.integer(griddim), PACKAGE = "affy")[[1]], nprobes,
nchips)
where the data are passed off to a C function. Right before that step
you can test the objects 'allx', 'ally' and 'nprobes' for any NA values.
Note here that while in the debugger, R shows you the *next* line it is
going to interpret, so when you see the above line you can test those
objects for the presence of NA values.
Let us know what you find!
Best,
Jim
>
> 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.
>> 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
>>
>
> _______________________________________________
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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.
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
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