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).

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*