Performance Evaluation of Transcriptomics Data Normalization for Survival Risk Prediction

TL;DR

This study evaluates how different normalization methods affect survival risk prediction from transcriptomics data, revealing that median and variance stabilizing normalization outperform the commonly used quantile normalization.

Contribution

The paper introduces a benchmarking tool for assessing normalization methods specifically in survival prediction, highlighting the importance of normalization choice in downstream analysis.

Findings

Handling effects significantly impact survival prediction accuracy.

Quantile normalization underperforms compared to median and variance stabilizing normalization.

Normalization evaluation should consider the specific downstream analysis context.

Abstract

One pivotal feature of transcriptomics data is the unwanted variations caused by disparate experimental handling, known as handling effects. Various data normalization methods were developed to alleviate the adverse impact of handling effects in the setting of differential expression analysis. However, little research has been done to evaluate their performance in the setting of survival outcome prediction, an important analysis goal for transcriptomics data in biomedical research. Leveraging a unique pair of datasets for the same set of tumor samples-one with handling effects and the other without, we developed a benchmarking tool for conducting such an evaluation in microRNA microarrays. We applied this tool to evaluate the performance of three popular normalization methods-quantile normalization, median normalization, and variance stabilizing normalization-in survival prediction using various approaches for model building and designs for sample assignment. We showed that handling effects can have a strong impact on survival prediction, and that quantile normalization, a most popular method in current practice, tends to underperform median normalization and variance stabilizing normalization. We demonstrated with a small example the reason for quantile normalization's poor performance in this setting. Our finding highlights the importance of putting normalization evaluation in the context of the downstream analysis setting and the potential of improving the development of survival predictors by applying median normalization. We make available our benchmarking tool for performing such evaluation on additional normalization methods in connection with prediction modeling approaches.