[BioC] probe exclusion in Affy - problem with Removeprobes function

[mahulchakraborty at rochester.edu]

Hello,
I have been trying to remove >50,000 probes from the Drosophila cdf environment (Affy package) using the Removeprobes function written by Ariel Chernomoretz. However, I ran into the same problem as posted six years ago by Benjamin Otto in the Bioconductor mailing list. I get the error message "Error in ans[[i]][, i.probes] : incorrect number of dimensions" after the "  > pmIndex <-unlist(indexProbes(newAB,"pm"))" line in the function. I followed the suggestions Ariel mentioned following Benjamin's post but still can't resolve it. Since Benjamin did get rid of this problem (as he had mentioned in his final post - https://stat.ethz.ch/pipermail/bioconductor/2005-December/011354.html) I am wondering if I have been missing any subtle point. Although it has been quite sometime since this issue was discussed I would be immensely grateful if Ariel, Benjamin or anyone else could share the solution/suggestions with me.
Please let me know if more details are needed on the problem.
Thanks and regards,

Mahul Chakraborty

Graduate Student
Department of Biology
University of Rochester