[BioC] Problem with affy mas5 on Linux but not Windows...
James Carman
james at carmanconsulting.com
Fri Jan 28 18:47:34 CET 2011
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
>
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