[BioC] Q: phantom probsets created by combineAffyBatch?

[C. Charles Gu]

Dear ALL,

Please forgive me if this is a known bug or a FAQ:  

Problem: 
(1) newcdf created by combineAffyBatch contains
genenames/probsets that are not common to the
batches being combined;  
(2) seemingly arbitrary values were assigned for 
these "phantom" probesets in the merged exprSet
to some of the columns/chips.

Chip versions:
hgu133a (22283 affyids) and 
hgu133a2 (22277 affyids)

The combined new batch has 22280 affyids, with
3 "phantom" probesets in newcdf:
[1] "AFFX-r2-Hs18SrRNA-3_s_at" "AFFX-r2-Hs18SrRNA-5_at"  
[3] "AFFX-r2-Hs18SrRNA-M_x_at"

Program versions (on a linux server):
R 2.0.1
Bioconductor 1.5.0
matchprobes 1.0.12

Any insights will be appreciated!

PS. This is actually not a serious problem for me because
the phantom probsets are affy "controls". But it'd be nice
if someone already has the answer before I read into the
codes of matchprobes. And may I also add that it's truely 
great to have something like matchprobes around!

Cheers, --Charles
______________________________________________________________
**************************************************************
C. Charles Gu, Ph.D.
Division of Biostatistics
Washington University School of Medicine
Campus Box 8067 660 S. Euclid Ave.
St. Louis, MO 63110-1093

Phone:  (314) 362-3642
Fax:    (314) 362-2693
E-mail: gc at wubios.wustl.edu
URL:    http://www.biostat.wustl.edu/faculty_staff/guchi.shtml