Figure 6.

Differentially expressed genes with duplicates treated as separate datasets. Heatmaps of genes found to be differentially expressed in each of the A and B replicate datasets of samples and the overlap after quantile normalisation (top) and ComBat batch-correction (bottom). The batch in which each sample was present is denoted by bar beneath the dendrogram, in which the run-colours are consistent with those in Figure 1, and the sample-type is illustrated by the blue bar (light = post-treatment, dark = pre-treatment). The numbers of probes differentially expressed in both A and B ('A&B') or 'A' only and 'B' only are shown in brackets. Sample clustering (by complete linkage) in each heatmap was determined by only those probes in the 'A&B' group.

Kitchen et al. BMC Genomics 2010 11:134   doi:10.1186/1471-2164-11-134
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