I found some candidate alternatively spliced exons in a paper by Gardina et al. (2006) that are annotated by so-called "probeset IDs" from the GeneChip Human Exon 1.0 ST array (e.g. "2425850" for a probeset of the gene COL11A1).
Now I would like to look for these candidates in my own data which, however, is annotated with Ensembl Exon IDs (e.g. "ENSE00001841506" of the gene COL11A1). There must be a possibility to map the probeset IDs from Gardina et al. to Ensembl Exon IDs (the mapping doesn't necessarily have to be unique) but somehow I can't find it. I would be very grateful for any pointers in the right direction!
Have you tried downloading a probeset annotation file from Affymetrix ?
I might be wrong but I don't think that Ensembl Exon IDs are included in the annotation files from Affymetrix - at least, there is no information about any kind of Ensembl ID in the Affymetrix NetAffx "Direct Access To Probe Set Information": https://www.affymetrix.com/LinkServlet?probeset=2425850