7.2 years ago by
Ask any two bioinformaticians about microarray normalisation and you'll get 10 different answers :-)
A good summary of MAS5 versus RMA is provided in the article 'Summaries of Affymetrix GeneChip probe level data'. A slightly-less technical, but comprehensive review can be found in this PPT presentation. The essential differences between RMA and MAS5 are:
- MAS5 normalises each array independently and sequentially; RMA as the name suggests (robust multi-array) uses a multi-chip model
- MAS5 uses data from mismatch probes to calculate a "robust average", based on subtracting mismatch probe value from match probe value
- RMA does not use the mismatch probes, because their intensities are often higher than the match probes, making them unreliable as indicators of non-specific binding
- RMA values are in log2 units, MAS5 are not (so values are not directly comparable)
In the literature, you will always be able to find examples where people state that one method performed better than another; here's an article extolling the virtues of MAS5. The important thing to remember is that they observed the improvement precisely once, under a specific set of conditions - you can't generalise to all cases from one good result.
In general though, I disagree with your colleague: I'd say that RMA "is more often used nowadays."
I suggest searching the Web (Google for "rma mas5"), reading some of the literature (the journal Bioinformatics is a good source for these types of articles) and browsing the Bioconductor mailing list to get at least a feel for the discussion around different methods.