Integrating functional genomics data using maximum likelihood based simultaneous component analysis

In contemporary biology, complex biological processes are increasingly studied by collecting and analyzing measurements of the same entities that are collected with different analytical platforms. Such data comprise a number of data blocks that are coupled via a common mode. The goal of collecting this type of data is to discover biological mechanisms that underlie the behavior of the variables in the different data blocks. The simultaneous component analysis (SCA) family of data analysis methods is suited for this task. However, a SCA may be hampered by the data blocks being subjected to different amounts of measurement error, or noise. To unveil the true mechanisms underlying the data, it could be fruitful to take noise heterogeneity into consideration in the data analysis. Maximum likelihood based SCA (MxLSCA-P) was developed for this purpose. In a previous simulation study it outperformed normal SCA-P. This previous study, however, did not mimic in many respects typical functional genomics data sets, such as, data blocks coupled via the experimental mode, more variables than experimental units, and medium to high correlations between variables. Here, we present a new simulation study in which the usefulness of MxLSCA-P compared to ordinary SCA-P is evaluated within a typical functional genomics setting. Subsequently, the performance of the two methods is evaluated by analysis of a real life Escherichia coli metabolomics data set.