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Affymetrix Permutation-based Probe Level Estimation (APPLE). Goal: Because of its cost, microarray experiments are frequently designed using a relatively small number of biological or technical replicates. This can result in low statistical power when the number of differentially expressed genes is inferred. This worklfow investigates whether the statistical power of Affymetrix experiments can be increased, without the need to increase the number of hybridizat...