[BioC] Problems using pdInfoBuilder to create an Affymetrix Mouse Diversity annotation package
beniltoncarvalho at gmail.com
Thu Dec 16 14:18:23 CET 2010
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).
> 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)
>>  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>>  LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>>  LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
>>  LC_PAPER=en_US.UTF-8 LC_NAME=C
>>  LC_ADDRESS=C LC_TELEPHONE=C
>>  LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>> attached base packages:
>>  stats graphics grDevices utils datasets methods base
>> Thanks a lot for your help, and best regards,
>> Bioconductor mailing list
>> Bioconductor at r-project.org
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