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

Christoph Standfuß christoph.standfuss at inf.fu-berlin.de
Thu Dec 16 13:44:29 CET 2010

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)

  [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

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

Thanks a lot for your help, and best regards,


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