BABAR -generated boxplots showing Salmonella gene expression for the dataset of Hautefort et al. . The figures plot M-value versus microarray identity. Gene expression values were obtained for Salmonella internalised in epithelial cells (dark grey boxplots), grown in Luria-Bertani broth (LB) control samples (white boxplots) or internalised in macrophages (light grey boxplots) prior to BABAR processing (A), and after background correction with 'within arrays' block-by-block data centering (B), cyclic loess with averaging of the log2-ratios (C), and final centering of the data representing the processed output of BABAR (D). Each box highlights the median and characterises the range of 50% of the data for each microarray; circles show individual genes that are outliers. Gene expression levels in epithelial cells were determined at 2 h (microarrays 1-4), 4 h (5-6) and 6 h (7-10) post infection (p.i.), for a mid-log LB culture (11-12), and in macrophages at 4 h (16-19), 8 h (20-23) and 12 h (13-15) p.i.