Summary
Objectives:
Discussion of different error concepts relevant to microarray experiments. Review
of some commonly used multiple testing procedures. Comparison of different approaches
as applied to gene expression data.
Methods:
This article focuses on familywise error rate (FWER) and false discovery rate (FDR) controlling procedures. Methods under investigation include: Bonferroni-type methods
and their improvements (including resampling approaches), modified Bonferroni methods,
data-driven approaches, as well as the linear step-up method and its modifications.
Particular emphasis lies on the description of the assumptions, advantages and limitations
for the investigated methods.
Results: FWER controlling procedures are often too conservative in high dimensional screening studies.
A better balance between the raw P-values and the stringent FWER-adjusted P-values may be required in many situations, as provided by FDR controlling and related procedures.
Conclusions:
The questions remain open, which error concept to apply and which multiple testing
procedure to use. Although we believe that the FDR or one of its variants will be applied more often in the future, longterm experience
with microarray technology is missing and thus the validity of appropriate multiple
test procedures cannot yet be assessed for microarray data analysis.
Keywords
Familywise error rate - false discovery rate - error concepts - screening
