Figure 9
From: Effect of various normalization methods on Applied Biosystems expression array system data
Differential expression t-test, t-test + FDR, t-test + FC, t-test + FDR + FC cut, SAM applied to Quantile normalization: we use different methods to detect significantly differentially expressed genes for different normalization methods: (1) t-test (p-value < 0.05), (2) t-test controlling FDR at 5% level, (3) t-test (p-value < 0.05) and FC < 1.5, (4) t-test controlling FDR at 5% level and FC < 1.5, or (5) SAM q < 0.05. We compare the results for data generated by site 1, from each normalization method, with the ones from TaqMan® assays for which differential expression is detected using t-test and controlling FDR at 5% level. We keep track of up/down regulation in each platform.