ReadMe, FinalOutput_Breast.RData contains the results from the subtype-specific analysis in breast cancer, including the results of the permutation-based procedure to compute p values and q values for the SAPSscores. allPs Contains raw p values for 5320 genesets in molsigdb.v3.0. The columns indicate the type of p value (P_pure, P_random, P_gsea) and the analysis that generated the p value (Global = “Global analysis”, ER_H = “ER+ High proliferation”, ER_L = “ER+ Low proliferation”, H2 = “HER2+”,TN = “ER-/HER2-“). These p values were generated on the subtype-specific scaled data. allPs.adj Matrix contains the adjusted p values using the method of Benajmini and Hochberg on the subtype-specific scaled data. saps.p Permutation-based p value for each gene set in molsigdb generated on the subtype-specific scaled data saps.p.adj Adjusted p value (q-value) to indicate the statistical significance of each gene set’s SAPSScore saps.score This matrix contains the maximum of each gene set’s raw (P_pure, P_random, P_gsea) saps.score.adj This matrix contains the maximum of gene set’s adjusted (P_pure, P_random, P_gsea) saps.score.r Array of dimensions 8 x 10000 x 6. The first dimension is the 8 sizes (from 5 to 250) of the random gene sets. The second dimension is the 10000 permutations. The third dimension is the 6 breast cancer analyses performed (Global and the 5 subtypes). Each cell in the array contains the SAPSScore obtained with a permuted gene set.