[BioC] Problem with affy mas5 on Linux but not Windows...
James W. MacDonald
jmacdon at med.umich.edu
Fri Jan 28 19:04:26 CET 2011
What do you get from traceback()?
On 1/28/2011 12:47 PM, James Carman wrote:
> I tried what you recommended:
>
>> library(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)'.
>
>> aff = ReadAffy()
>> any(is.na(exprs(aff)))
> [1] FALSE
>> 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)
>
> So, no NA values in my data.
>
> On Fri, Jan 28, 2011 at 12:41 PM, James W. MacDonald
> <jmacdon at med.umich.edu> wrote:
>>
>> 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
>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>>
>>>
>>> _______________________________________________
>>> 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
>>
>
> _______________________________________________
> 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
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