microarry data - (May/21/2010 )

I tried to look for some related data from the public microarray database. I found out for the gene I am interested in there are two probes associated with that and the results are different between two data sets. The first probe covers intron-exon junction and the other one only covers part of the exon. I think the data from the first probe is more reliable. Is it true? I am looking forward to hear some expert suggestions. Thanks!

Your assumption may not necessarily be true. The discrepany may be resulted from splicing isoforms, hybridization efficiency, etc.