[[Apologies in advance since this may be an off topic subject but I have tried hard without finding any consensus.]] Problem: I am trying to combine data from Affymetrix platform and non-Affymetrix platform (most of them two-color technologies) from the raw data (e.g. CEL, GPR). Therefore I need to find the choice of "compatible" preprocessing for Affy and non-Affy. I found 3 studies trying to combine Affy with non-Affy. Irizarry et al (PMID:15846361) uses RMA for Affy and print-tip normalization with no background correction. Larkin et al (PMID:15846360) uses Li-Wong for Affy and LOWESS followed by z-scoring between array subgrids. I am unclear how Brammler et al (15846362) preprocessed their data (although one of the supplementary alludes to MAS 5.0 for Affymetrix). Therefore, I have decided to use RMA for Affy and LOESS normalisation followed by z-scoring (i.e. zero mean, unit variance) the columns/arrays for non-Affy platforms. Question: Can anyone kindly point me to any other papers that tries to address this question? Can anyone comment/correct me on my decision? Any other suggestions kindly welcome. Thank you. Regards, Adai