Batch effect and probe GC content. TOP: A, histogram of GC content over our Illumina HT-12 probes; B, gaussian-smoothed probability density distribution (black, N = 48,803). Union of probes more than 2-fold up- or down-regulated due to the batch effect in any of the 14 duplicate tumour-sample pairs from Additional File 4 (green line, N = 2,661). Union of probes more than 2-fold up- or down-regulated due to the batch effect in more than 5 of the duplicate tumour pairs (red line, N = 207). BOTTOM: Plots of probe CG-fraction against standard deviation estimated at the inter-experiment (A), inter-run (B), and inter-chip (C) levels in our combined Illumina Ref-8/HT-12 dataset. Red lines denote the cutoff s used in chi-squared analysis at each level.