New figures of merit for comprehensive functional genomics data: the metabolomics case

In the field of metabolomics, hundreds of metabolites are measured simultaneously by analytical platforms such as gas chromatography/mass spectrometry (GC/MS), liquid chromatography/mass spectrometry (LC/MS) and NMR to obtain their concentration levels in a reliable way. Analytical repeatability (intrabatch precision) is a common figure of merit for the measurement error of metabolites repeatedly measured in one batch on one platform. This measurement error, however, is not constant as its value may depend on the concentration level of the metabolite. Moreover, measurement errors may be correlated between metabolites. In this work, we introduce new figures of merit for comprehensive measurements that can detect these nonconstant correlated errors. Furthermore, for the metabolomics case we identified that these nonconstant correlated errors can result from sample instability between repeated analyses, instrumental noise generated by the analytical platform, or bias that results from data pretreatment.