Table 2.

Methods under Evaluation. Summary of the six methodologies for oligonucleotide array data that were compared in this study. Details on the methodologies can be found in the references. An asterisk (*) marks components of methods that were studied in the follow-up analysis (see Table 5).

Method	Background Adjustment	Normalization	Mismatch adjustment	Probeset Summary	Reference
MAS5	regional adjustment*	scaling by a constant*	subtract idealized mismatch*	Tukey biweight average*	[17]
gcRMA	by GC content of probe*	quantile normalization*	PM only*	medianpolish* (robust fit of linear model)	[9]
RMA	whole array adjustment	quantile normalization*	PM only*	medianpolish* (robust fit of linear model)	[2]
VSN	none*	variance stabilizing transformation	PM only*	medianpolish* (robust fit of linear model)	[18]
dChip	none*	invariant set*	PM only*	Li-Wong multiplicative	[19]
dChip.mm	none*	invariant set*	subtract mismatch*	model*