Figure 9.

Sensitivity of comparing protein abundance between conditions. Sensitivity of comparing protein abundance between conditions as described at the beginning of Section 3. (a) Study of breast cancer cell lines. (b) Study of subjects with osteosarcoma. X-axis: p-values adjusted to control for the FDR using the approach by Benjamini and Hochberg. Y-axis: number of significant proteins. Solid black line: the proposed joint modeling of all conditions. Dashed red line: a linear mixed effects model that represents the conditions of interest, and ignores the rest of the data. Dashed green line: a naïve analysis, which averages feature intensities in each replicate and uses a t-test for significance analysis.

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