[BioC] Problems using pdInfoBuilder to create an Affymetrix Mouse Diversity annotation package

[Christoph Standfuß]

Hi Benilton,

sorry for my late reply. So I tried it with R 2.12 and 2.10.x and it is 
always the same problem.

If I run R 2.12 and try to create the package using

 > makePdInfoPackage(pkg, destDir = wd)

I get

Creating package in 
/media/0C025E96391493AF/data/FSP_Klein_Pospisil/pd.mousedivm520650
Error in is(object, Cl) :
   error in evaluating the argument 'bind.data' in selecting a method 
for function 'dbSendPreparedQuery'
Timing stopped at: 22.797 6.852 30.105

And traceback() gives this result:

 > traceback()
9: is(object, Cl)
8: .valueClassTest(standardGeneric("dbSendPreparedQuery"), "DBIResult",
        "dbSendPreparedQuery")
7: dbSendPreparedQuery(db, sql, data.frame(pmi = batchMat[isPm,
        "indices"], mmi = batchMat[!isPm, "indices"]))
6: loadUnits(db, qcunits, isQc = TRUE)
5: loadUnitsByBatch(db, cdfFile, batch_size = batch_size)
4: ST(loadUnitsByBatch(db, cdfFile, batch_size = batch_size))
3: buildPdInfoDb(object at cdfFile, object at csvAnnoFile, object at csvSeqFile,
        dbFilePath, seqMatFile, batch_size = batch_size, verbose = !quiet)
2: makePdInfoPackage(pkg, destDir = wd)
1: makePdInfoPackage(pkg, destDir = wd)


My SessionInfo is:

 > sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i686-pc-linux-gnu (32-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] pdInfoBuilder_1.14.1 oligo_1.14.0         oligoClasses_1.12.1
[4] affxparser_1.22.0    RSQLite_0.9-4        DBI_0.2-5
[7] Biobase_2.10.0

loaded via a namespace (and not attached):
[1] affyio_1.18.0         Biostrings_2.18.2     IRanges_1.8.5
[4] preprocessCore_1.12.0 splines_2.12.0


Thanks,
Christoph

On 12/16/2010 02:18 PM, Benilton Carvalho wrote:
> Or, given that you tried with R 2.12, can you please give me the exact
> sessionInfo() for that?
>
> On 16 December 2010 13:17, Benilton Carvalho<beniltoncarvalho at gmail.com>  wrote:
>    
>> Can you please update to the latest R and pdInfoBuilder and let us
>> know if the error persists?
>>
>> Also, note that, although you'll have the annotation package, you
>> won't be able to get genotype calls through oligo/crlmm (currently, we
>> need training data to train the algorithm).
>>
>> b
>>
>> On 16 December 2010 12:44, Christoph Standfuß
>> <christoph.standfuss at inf.fu-berlin.de>  wrote:
>>      
>>> Hello, everyone
>>>
>>> I am currently analysing a couple of Affymetrix Mouse Diversity Genotyping
>>> Arrays. Unfortunately there is no annotation package available yet. So I
>>> tried to create an own annotation package using pdInfoBuilder, the CDF and
>>> annotation files provided by Affymetrix library files.
>>>
>>> I followed the instructions, given in the manual. Whenever I select
>>> "AffySNPPDInfoPkgSeed" as package class, I get the error:
>>>
>>>        
>>>> makePdInfoPackage(pkg, destDir = wd)
>>>>          
>>> Creating package in /media/0C025E96391493AF/data/FSP/pd.mousedivm520650
>>> Error in data.frame(pmi = batchMat[isPm, "indices"], mmi = batchMat[!isPm,
>>>   :
>>>   arguments imply differing number of rows: 28132, 19132
>>> Error in is(object, Cl) :
>>>   error in evaluating the argument 'bind.data' in selecting a method for
>>> function 'dbSendPreparedQuery'
>>> Timing stopped at: 22.109 7.016 29.95"
>>>
>>>
>>>
>>> I guess the problem might be that Bioconductor is not able to handle the CDF
>>> file correctly? I tried R 2.10.* (bioconductor 2.5) and R 2.12 (bioconductor
>>> 2.7), but I had always the same problems.
>>>
>>> My sessionInfo() is
>>>
>>> R version 2.10.1 (2009-12-14)
>>> i686-pc-linux-gnu
>>>
>>> locale:
>>>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>>   [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>>>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> Thanks a lot for your help, and best regards,
>>>
>>> Christoph
>>>
>>> _______________________________________________
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>>>
>>>        
>>