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

[Benilton Carvalho]

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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