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Principal component analysis. Scatter plot of Principal Component Analysis (PCA) of the 5,000 most variable probes across batches without transformation, transformed by ComBat, and transformed to the MIRT: Old Kit standard by M-ComBat. Grey data ellipse seen in ComBat panel represents untransformed MIRT: Old Kit. After transformation by M-ComBat, the differences in location between the batches has been eliminated and all batches coincide with the desired MIRT: Old Kit standard.
