Evaluation of procedures for normalizing and analysing SomaScan proteomics assay

Abstract The aptamer-based SomaScan assay measures thousands of proteins. SomaLogic provides a multi-step pre-processing procedure to reduce the technical variability of this data. This paper will evaluate how each step of this procedure affects analysis results. We performed a comparative assessment using data from two randomised clinical trials in weight management. We show that SomaLogic’s adaptive normalization by maximum likelihood (ANML) procedure introduces a bias to fold change estimates, with a median bias of + 3.7% and + 3.4% in the two trials. The bias was confirmed by a simulation study, where ANML introduced false positive findings. Additionally, their plate scaling procedure has no effect on data when the calibration step is included. However, SomaLogic's pipeline excluding ANML does reduce technical variability without a substantial impact on fold change estimates. We recommend that researchers considering the use of ANML in clinical trials should verify the absence of this bias.