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