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Figure 2 | BMC Bioinformatics

Figure 2

From: Cross-platform comparability of microarray technology: Intra-platform consistency and appropriate data analysis procedures are essential

Figure 2

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 [11] 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.

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