Additional file 2.

A) Boxplots showing the range of Pearson correlation coefficients between 18 matched samples (including baseline, 14-day and 3 month from 6 patients) for different correction methods. B) Affymetrix dataset and C) Illumina dataset boxplots showing the range of Pearson correlation coefficients between all possible sample combinations for different correction methods. D) Boxplots of standard deviation for each gene across all samples from the same subgroup (baseline and 3 months) for Affymetrix and Illumina datasets independently and when combined both before and after correction with either ComBat or XPN. E) Hierarchical clustering of samples based on Pearson correlation after either ComBat or XPN correction. Colour denotes samples from the same patient, the suffixes on patient ID’s denote as follows: ‘.1’ = Baseline, ‘.2’ = 14-day and ‘.3’ = 3 months.

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Turnbull et al. BMC Medical Genomics 2012 5:35   doi:10.1186/1755-8794-5-35