The operons, a criterion to compare the reliability of transcriptome analysis tools

The number of statistical tools used to analyze transcriptome data is continuously increasing and no one, definitive method has so far emerged. There is a need for comparison and a number of different approaches has been taken to evaluate the effectiveness of the different statistical tools available for microarray analyses. In this paper we describe a simple and efficient protocol to compare the reliability of different statistical tools available for microarray analyses. It exploits the fact that genes within an operon exhibit the same expression patterns. We have compared five statistical tools using Bacillus subtilis expression data: ANOVA, PCA, ICA, the t-test and the paired t-test. Our results show ICA to be the most sensitive and accurate of the tools tested.