[BioC] Problem with affy mas5 on Linux but not Windows...
James Carman
james at carmanconsulting.com
Fri Jan 28 20:49:03 CET 2011
I'm willing to do some work. I'm just a bit green when it comes to R,
so your requests were a bit daunting at first. Your instructions seem
thorough enough, though. So, perhaps I'll try it out. For right now,
I've just turned off background correction and I'm getting all of my
downstream processing stuff working with the resulting data from that.
However, we definitely need background correction, so I need to fix
this issue. I thank you for being so helpful. I'll report back what
I find or if I have further questions.
Anyone have any good suggestions as far as books on R are concerned?
I need to get a good tutorial/reference book. I'm a Java guy, but
have been asked to do this R stuff by my client, so I'm trying to
blindly feel my way around.
On Fri, Jan 28, 2011 at 2:39 PM, James W. MacDonald
<jmacdon at med.umich.edu> wrote:
> So it is as I surmised. Somehow or another you are ending up with NA values
> in the data passed to the underlying C code. This is 99.9999999% likely to
> be due to problems with your data, as literally thousands of people have
> used this function without problems.
>
> I don't know how to help you any more than I have. You don't seem interested
> in running the debugger on bg.correct.mas(), and without any more
> information than I already know, I am stuck.
>
> So unless you are willing to do some work on your end, my best suggestion is
> to use your Windows box.
>
> Best,
>
> Jim
>
>
>
> On 1/28/2011 1:07 PM, James Carman wrote:
>>>
>>> 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
>>>
>
> --
> 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
>
More information about the Bioconductor
mailing list