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

James Carman james at carmanconsulting.com
Fri Jan 28 19:07:50 CET 2011 

> traceback()
10: .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")
9: as.vector(data)
8: 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)
7: bg.correct.mas(object, ...)
6: do.call(methodname, alist(object, ...))
5: function (object, method, ...)
   standardGeneric("bg.correct")(afbatch, method = bgcorrect.method)
4: function (object, method, ...)
   standardGeneric("bg.correct")(afbatch, method = bgcorrect.method)
3: do.call(affy:::bg.correct, c(alist(afbatch, method = bgcorrect.method),
       bgcorrect.param))
2: expresso(object, bgcorrect.method = "mas", pmcorrect.method = "mas",
       normalize = FALSE, summary.method = "mas", ...)
1: mas5(aff)


On Fri, Jan 28, 2011 at 1:04 PM, James W. MacDonald
<jmacdon at med.umich.edu> wrote:
> 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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