Density plots of MSQwithin (blue) and MSQbetween (red). MSQs were calculated based on the gene expression measured for the three sample groups analyzed, namely untreated HaCaT cells after 2, 4, and 12 hours. The grey dashed line indicates the expected value for the MSQbetween of 1.33 based on 6, 6, and 7 as measurements for the group means of four replicates for three time points. Three examples of different quality are shown. Based on the noBg_vst_loess pre-processing the MSQwithin values show a strong bimodal distribution, for the bg_rma_log_rsn pre-processing the distribution is very asymmetric. The distributions for noBg_log_rsn based values reflect the desired behaviour. The quality values assigned are -2, 0, and 2, for noBg_vst_loess, bg_rma_log_rsn, and noBg_log_rsn, respectively. For an overview of the distributions for all pre-processing methods and their respective plots, see Additional file 2.
Schmid et al. BMC Genomics 2010 11:349 doi:10.1186/1471-2164-11-349