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Comparing MAS5 and RMA.mp4
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There are several ways of gene-level-quantification for Affymetrix 3'-IVT GeneChip data. MAS5 is the oldest algorithm, and RMA is one of lately developed ones.

Some people say MAS5 and RMA data are not comparable. Some people say RMA is more reliable than MAS5. And others say RMA is a trick to make data quality good.

But no algorithm is free from biasing. What's important is to know character of them so that you can select proper one for your purpose. You can download the SSA file to examine by yourself.

SSA Download:
https://www.sugarsync.com/pf/D664412_7039661_700749

Data Source:
"Inflammation, adenoma and cancer: objective classification of colon biopsy specimens with gene expression signature."
http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.c​gi?acc=GSE4183
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