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Different gene-set scores by excluding components corresponding to unwanted variance. The BH corrected p value of cell cycle checkpoint pathway (REACTOME) is increased, by excluding a component well correlated with cell doubling time (component 1). The corrected p value increased from <10−12 to >10−3 in MCF7 and MDA_MB_231 cells because component 1 is significantly associated with cell doubling time in these cell lines (see supplemental Fig. S13).
