Figure 10.

Corra generated volcano plot of yeast phosphopeptide analyses. Phosphopeptides were isolated from two yeast strains, one wild type, and the other an Ark1 protein kinase knockout, and analyzed in triplicate on a very high mass accuracy LC-MS platform, as described under Methods. Volcano plot displays 22,562 features that aligned across 3 or more LC-MS runs. The x-axis shows observed log fold change in aligned feature mean intensities between the two yeast strains. The y-axis shows B-statistics log Odds for non-random differential abundance obtained for each aligned feature. Red colored dots indicate features with a log Odds value of ≥ 2.2 (which translates to a posterior probability of 90% chance of non-random differential abundance) and that also utilized the 'n/a replace' capability in Corra (for missing values). Blue colored dots indicate features with a log Odds value of ≥ 2.2, but did not require use of the 'n/a replace' function. A log Odds value of 0 corresponds to a 50% probability of non-random differential abundance, and a log Odds of 2.2 to a 90% probability.

Brusniak et al. BMC Bioinformatics 2008 9:542   doi:10.1186/1471-2105-9-542
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