Intra and Inter-run comparisons of clinical duplicates. Mean Pearson-correlations between replicate pairs of tumour samples (A and B) on different chips and runs. Colours denote the four different data types; raw, quantile normalised (QN), quantile normalised then mean centred (QN+MC), and quantile normalised then ComBat corrected (QN+CB). Expressions were generally highly correlated except in the chips straddling runs 4 and 5. ComBat is able to correct for a significant amount of this difference. Error bars represent the standard error.