Fig. 2

Batch correction allows robust direct integration of transcriptomic data across platforms. a Dissimilarity heatmaps based upon Pearson correlations ranging from 0.4 (red) through shades of orange and yellow to 1.0 (white). Left triangle shows the combined dataset of 6844 genes across 7 gene expression platforms. Right triangle shows the same data following batch correction with Combat. Coloured bars below dendrograms denote the platform. b Enlargement of the dendrogram to demonstrate that the majority of the same time-point patient samples processed on different platforms cluster together following batch correction. c Scatter plots before (grey) and after batch correction (pink) of the same sample, either FF or FFPE processed across different platforms. In each case the Pearson correlations increase substantially following batch correction. Patient samples are denoted − 1 for pre-treatment, − 2 for early on-treatment