[BioC] Problems with Affy names / BGA

[Heike Pospisil]

Dear list,

I am dealing with between group analysis (BGA) from the made4 package 
and I have a problem with some of the affy names:

I tried
bga.suppl(training.set[list,], supdata=test.set[list,], 
classvec=cl_train, supvec=cl_test)

'training.set' and 'test.set' are expression sets, and 'cl_train' and 
'cl_test' the corresponding classification vectors.

'list' contains some selected affy IDs.
 >list
[1] "217367_s_at"  "202880_s_at"  "1565905_at"   "236347_at"    ...

I tried bga with different lists, and in most cases, this works fine. 
But however, sometimes the following error message appears:
Error in "dimnames<-.data.frame"(`*tmp*`, value = list(c("217367_s_at",  :
         invalid 'dimnames' given for data frame

It has definitively to do with the selected identifiers, and I have the 
impression that made4 can not manage identifiers with an minus sign 
inside, such as:
AFFX-HUMGAPDH/M33197_M_at
AFFX-BioDn-3_at

I am running
ade4 (Version: 1.4-2) and made4 (Version: 1.8.0) under R 2.3.1

Has somebody an idea how to handle this problem?

Thanks in advance,
Heike
-- 
Dr. Heike Pospisil      | pospisil at zbh.uni-hamburg.de
University of Hamburg   | Center for Bioinformatics
Bundesstrasse 43        | 20146 Hamburg, Germany
phone:+49-40-42838-7303 | fax: +49-40-42838-7312