Volcano plots. Log2 ratios and p-values for the comparison of untreated HaCaT cells at 4 hours compared to 2 hours, 12 hours compared to 2 hours, and 12 hours compared to 4 hours were calculated based on the gene expression measured. Three examples of different qualities are displayed showing the -log10(p-value) against log2 ratio comparing 4 hours to 2 hours. The blue line represents a loess-curve fitted to the values. Quality values assigned to bg_rma_log_rsn, noBg_log_loess, and noBg_log_rsn are -2, 0, and 2, respectively. Pre-processing using bg_rma_log_rsn yields a very flat volcano like shape with p-values exhibiting a high degree of scattering, i.e. log2 ratios are overestimated and at the same time p-values are not very accurate. In contrast, noBg_log_loess better represents the expected range of log2 ratios (not many genes are assumed to heavily change their expression between different time points) but compared to noBg_log_rsn p-values still are not very accurate, i.e. show a high degree of scattering for equivalent log2 ratios. For a complete overview over all methods and all comparisons, see Additional file 3.
Schmid et al. BMC Genomics 2010 11:349 doi:10.1186/1471-2164-11-349