Hi all,
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
I don't quite understand your problem. Could you try giving an actual example?
If a gene maps to 7 probes instead of 11, why is it incomplete?
I’m sorry for the unclear description. Most probe set of Affymetrix HG U133 plus 2.0 Array has 11 probes, and it use the signal of whole probe set (11 probes) to evaluate the expression level of each gene. I want to use the signal of part of probe (e.g. 7 probes) in a probe set to evaluate the gene expression level, because some genes I interested in can only be mapped with part of probes in a probe set.