Figure 3.

Exploratory data analysis in MSstats. Y-axis: Log-intensities, lines link log-intensities of LC-MS features, averaged over all replicates. (a) Quality control: profile plot of the protein SLC44A2 in the study of breast cancer cell lines. X-axis: all conditions. (b) Feature-level comparisons: trellis display of the protein SLC44A2 in the study of breast cancer cell lines. X-axis: one factor (time). Each panel: the combination of the other factors. (c) Feature-level comparisons for time course experiments: trellis display of the Entrez ID 28299 of the study of subjects with osteosarcoma. Each panel: a subject. X-axis: time.

Clough et al. BMC Bioinformatics 2012 13(Suppl 16):S6   doi:10.1186/1471-2105-13-S16-S6