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

BACKGROUND: The proteomics literature has seen a proliferation of publications that seek to apply the rapidly improving technology of 2D gels to study various biological systems. However, there is a dearth of systematic studies that have investigated appropriate statistical approaches to analyse the data from these experiments. RESULTS: Comparison of the effects of statistical pre-processing on the results of two sample t-tests suggests that the results of 2D gel experiments and by extension the conclusions derived from these experiments are not independent of the statistical protocol used. CONCLUSIONS: This study suggests that there is a need for well-conducted validation studies to establish optimal statistical techniques to be used on such data sets.