Integrative analysis of multi-omics data from different high-throughput experimental platforms provides valuable insight into regulatory mechanisms associated with complex diseases, and gains statistical power to detect markers that are otherwise overlooked by single-platform omics analysis. In practice, a significant portion of samples may not be measured completely due to insufficient tissues or restricted budget (e.g. gene expression profile are measured but not methylation). Current multi-omics integrative methods require complete data. A common practice is to ignore samples with any missing platform and perform complete case analysis, which leads to substantial loss of statistical power.