Statistical exploration of variation in quantitative two-dimensional gel electrophoresis

Two-dimensional gel electrophoresis is a major technique in global analysis at the proteinlevel. This paper presents an examination of spot volume data from three gel sets with radioactivelylabeled yeast Saccharomyces cerevisiae proteins. A strong variance versus meandependence in data was found to be stabilized by applying a shifted logarithmic transformation.However, transformed data showed a remaining substantial variance heterogeneity fordifferent proteins. Furthermore, examination of studentized residuals revealed that transformeddata were approximately normally distributed and that there were spatial correlationsamong the measurement errors in the gel