Multiple data-analytic methods have been proposed for evaluating gene-expression levels in specific biological pathways, assessing differential expression associated with a binary phenotype. Following Goeman and Bühlmanns recent review, we compared statistical performance of three methods, namely Global Test, ANCOVA Global Test, and SAM-GS, that test self-contained null hypotheses Via. subject sampling. The three methods were compared based on a simulation experiment and analyses of three real-world microarray datasets.