[BioC] Comparing/clustering data sets from two-color and single color array

[xiangxue Guo]

HI,

I want to compare two daya sets for clustering: one is from two-color array with log ratio; while another is raw data from single-color agilent array. my rerult has shown they are totally seperated groups in cluster or heatmap. 

Anybody has got known how to normalize and combine those two different data sets togather, to compare and cluster them?

Thanks,

Xiang