Skip to main content
Figure 1 | BMC Biotechnology

Figure 1

From: The case for well-conducted experiments to validate statistical protocols for 2D gels: different pre-processing = different lists of significant proteins

Figure 1

Statistical protocol for 2D gels. The first protocol that we followed in the statistical analysis of data from 2D gel experiments is demonstrated in the flowchart in Figure 1. This consists of: 1) testing for differences between the groups with respect to total protein expression; 2) normalizing protein intensities on a gel to the mean total intensity of its group (e.g. treatment or control); 3) expressing each normalized intensity as a fraction of the total protein intensity in the experiment in order to make fold change comparisons meaningful; 4) testing the distribution of normalized intensities and using appropriate transformations if necessary to convert distribution to a normal distribution; 5) selecting the subset of protein spots to analyse; 6) imputing values for missing spot intensities; 7) using 2-sample t-tests and f-tests to identify protein spots that can be used to build classifiers; 8) building a linear (or quadratic) discriminant classifier; and 9) using Principal Components Analysis plots to demonstrate the separation between groups visually.

Back to article page