As I understand it, X:Map is designed primarily to handle the 1.0 Exon arrays from Affymetrix. The 1.0 ST Human Gene arrays mostly lack the extended probe coverage that allows one to sort out differences between alternative splicing and so forth. That being said, the Human Gene 1.0 ST array has on it roughly 2,000 probe sets that target normal gene intronic regions. I am a little unclear why Affy left them in there, but I think it is reminiscent of the old "mismatch" probes on earlier generation arrays. I think the idea was, in both cases, that really nothing was meant to hybridize to these regions, so they could offer a handy measure of non specific binding. Or not. In our case, we see quite a nice signal from our intronic probes. In fact, differences in these intronic regions seems to correlate well with treatment, so a high proportion of our differentially expressed probes turn out to be intronic. This strikes me as odd, because I thought our isolation procedure would result in pretty pure mature mRNA. I'd also like to know what is on either side if the probes that are coming up. If this is unspliced pre-mRNA, than what gene does it belong to? Affy's annotations are mute on this subject, so I was wondering whether X:Map might be able to help out, even though, as I understand it, it really is not designed for the array I am using. Thanks awfully much. Tom