Table 5.

Components of Methods Examined in Follow-Up Analysis. The table gives abbreviations for the methods in Table 2 that are studied in the follow-up analysis. These abbreviations are used in RESULTS and Figures 6–9.

Method	Background Adjustment	Normalization	Mismatch adjustment	Probeset Summary	Reference
MAS5	BA-RA	constant	adjustedMM	TukeyAverage	[17]
gcRMA	BA-GC	quantile	PMonly	medianpolish	[9]
dChip.mm	BA-none	invariantset	subtractMM	Li-Wong	[19]