ROAST: rotation gene set tests for complex microarray experiments.

ABSTRACT:

Motivation

A gene set test is a differential expression analysis in which a P-value is assigned to a set of genes as a unit. Gene set tests are valuable for increasing statistical power, organizing and interpreting results and for relating expression patterns across different experiments. Existing methods are based on permutation. Methods that rely on permutation of probes unrealistically assume independence of genes, while those that rely on permutation of sample are suitable only for two-group comparisons with a good number of replicates in each group.

Results

We present ROAST, a statistically rigorous gene set test that allows for gene-wise correlation while being applicable to almost any experimental design. Instead of permutation, ROAST uses rotation, a Monte Carlo tech

SUBMITTER: Wu D 

PROVIDER: S-EPMC2922896 | biostudies-literature | 2010 Sep

REPOSITORIES: biostudies-literature