A question in 2 parts: 1. Are the "probeset base positions" in the meta-data packages (for the affy chips) derived explicitly from the affymetrix annotation provided by the company in their quarterly annotation files? 2. When there are multiple "base positions" mapped to a single probeset, is that due to the fact that there may be an overlapping transcript? Specifically I am referring to the case where one probeset seems to be annotated to multiple positions in the same general area of a single chromosome. See below for details. Thanks in advance, Neil Hayes using R - 1.9.0 geneplotter 1.4.0 hgu95av2 1.5.1 (downloaded today 5/24/04) I used the geneplotter package to generate an object of class "chromLocation" for the 95av2 chip. Next I extracted the chromosome locations as below: chrObj <- buildChromLocation("hgu95av2") ChromLoc <- chromLocs(chrObj) As described in the vignette for the package there are a limited number of probesets which are annotated to multiple chromosomes. What I did not see in the vignette was the phenomonon of many probesets (my analysis shows 908 probesets) being annotated to more than one locus on a chromosome. For example: probeset "1003_s_at" is mapped to 2 base positions on Chr 11 (118292218) and (118301752) The most current affy annotation (the csv file from the Affy web site) shows that "1003_s_at" is mapped to chr11: 118302397-118302992 with an overlapping transcript chr11:118301752-118303772. I suspect the disagreement may be that the R annotation is from March 2004 while the current Affy annotation was updated in April.