Hierarchical clustering of replicate sample pairs. Clustering was based on log ratios with average linkage and a distance metric of (1-LRr2), where LRr2 is the squared Pearson correlation coefficient between the log ratios. The numbers represent (1-LRr2), which approximately equals the percentage of uncommon genes. A: Clustering based on the expression profiles across 2009 genes (without data filtering); B: Clustering based on the expression profiles across 537 genes (with data filtering). There is a dramatic increase in LRr2 after filtering noisy data (note the different scales of the distance in each figure). Deficient technical and biological reproducibility on the Affymetrix platform from Tan's study  is evident. Technical reproducibility on the Agilent and Amersham platforms appears to be reasonable (B). However, although biological reproducibility can be high (e.g., B2 and B3 on Agilent), there appears to be a clear separation of sample B1 from samples B2 and B3.