Entering edit mode
Christoph Standfuß
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30
@christoph-standfu-4391
Last seen 10.5 years ago
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