Figure 1

Comparison of Affymetrix gene expression data generated using amplified and unamplified protocols. A, Comparing fold changes between unamplified and amplified datasets demonstrates reasonable correlation. B, Comparing fold changes across datasets (unamplified MCF7 with amplified MCF10A and vice versa) is clearly impractical (grey spots), however following mean batch-centering there is excellent correlation across the datasets (black spots). C, Comparison of mean raw expression levels for amplified and unamplified MCF10A replicates before (grey) and after mean batch-centering (black). D, Pearson clustering of the GeneChips representing the same cell lines is tighter following mean-centering. E, Mean-centering has no effect on fold changes between datasets. F, Mean-centering of unbalanced datasets (duplicate rather than triplicate amplified MCF10A) results in a distortion of the comparison (black spots), however this is rectified with weighted mean-centering (open dark grey spots), both methods show a dramatic improvement over uncorrected data (light grey spots).