Figure 4  Average of the fraction of genes shared by two lists of differentially expressed genes (overlap) as a function of the sample size using the Breast Cancer dataset divided according to (A) pre-operative treatment response (pCR, pathologic complete response) and (B) estrogen receptor (ER) endpoint. Each list of differentially expressed genes is composed by the top 100 genes chosen according to different ranking methods, i.e., t-test, SAM and LIMMA (preprocessed by the RMA method), and our approach (median t-value) which does not require a preprocessing algorithm. The average value of the overlap between the lists is calculated over 100 lists chosen randomly.