Gene selection and percentage of agreement in gene lists in simulated data sets. Illustrations of the effect of biological context, replicate CV distribution, gene list size, and gene selection rules/methods on the reproducibility of gene lists using simulated microarray data. In some sense, these three graphs represent some extremes as well as typical scenarios in differential expression assays. However, FC sorting with low P thresholds (0.001 or 0.0001; light and medium gray boxes) consistently performed better overall than the other rules, even when FC-ranking or P-ranking by itself did not perform as well.
Shi et al. BMC Bioinformatics 2008 9(Suppl 9):S10 doi:10.1186/1471-2105-9-S9-S10