Recently I am doing the analysis of comparison between microarray data and RNA-seq data.
There is a problem confused me a lot...
The array data I used is from Affymetrix Human Genome U133 Plus 2.0 array. The gene names I used are from refseq.
Affy do provide a mapping table from probe to refgene ID. But I find out that the mapping table is not one to one...
That is to say, one probe might correspond to several refgene IDs.. And one refgene ID also will corresponds to several probes.
My problem is that which expression value of the probe should I pick for the specific refgene ID?
Or, how to combine different probe expression data to represents the specific refgene ID expressions?