I'm trying to reannotate the probe of Affymetrix HG U133 plus 2.0 Array. I found some genes I interested in were mapped with less than 11 probes (for example 7 probes). I wanted to generate the expression value of these genes using the imcomplete probe set, but I don't know how to do it. One solution I can think of is to delete the unmapped probe information of the probe set targeting to the gene I interested in from CDF file, and then used the edited CDF file to generate the expression value using affymetrix Expression Console. I successed to generate the expression value using this strategy, but I found that the expression value seems to be positive correlated with the probe number in the probe set, that is, the more probe number I used, the higher expression value I will get. So, I'm not sure whether this solution can generate the right expression value or not. I would appreciate that if anyone can give me advice to handle this problem.
Best, Jian-You Liao