Non-parametric multivariate analysis of variance in the proteomic response of potato to drought stress

Spot detection is a mandatory step in all available software packages dedicated to the analysis of 2D gel images. As the majority of spots do not represent individual proteins, spot detection can obscure the results of data analysis significantly. This problem can be overcome by a pixel-level analysis of 2D images. Differences between the spot and the pixel-level approaches are demonstrated by variance analysis for real data sets (part of a larger research project initiated to investigate the molecular mechanism of the response of the potato to drought stress). As the method of choice for the analysis of data variation, the non-parametric MANOVA was chosen. NP-MANOVA is recommended as a flexible and very fast tool for the evaluation of the statistical significance of the factor(s) studied.