I have microarrays normalized with RMA algorithm (Affy GeneChip Rat 2.0 ST) and older microarrays RG U34A which were normalized with MAS5 algorithm (I have no raw data so I cannot reanalyze them just with RMA). Now I want to compare results (gene lists) and I think that a good idea is to normalize RG U34A with RMA algorithm.
Do you have any experience ?
Thank you for so comprehensive answer. These data were not from GEO, so it is impossible to obtain raw data.
I wanted to compare datasets normalized separately in the same way to be able to minimize the influence of any preprocessing influence to the results.
Now I am using cutoff thresholds for adj.p or for unadjusted P and Fold Change but It is very difficult to compare different experiments on brain tissue.
Maybe I will try with meta analysis.