RCRdiff: A fully integrated Bayesian method for differential expression analysis using raw NanoString nCounter data.

ABSTRACT: The medium-throughput mRNA abundance platform NanoString nCounter has gained great popularity in the past decade, due to its high sensitivity and technical reproducibility as well as remarkable applicability to ubiquitous formalin fixed paraffin embedded (FFPE) tissue samples. Based on RCRnorm developed for normalizing NanoString nCounter data and Bayesian LASSO for variable selection, we propose a fully integrated Bayesian method, called RCRdiff, to detect differentially expressed (DE) genes between different groups of tissue samples (eg, normal and cancer). Unlike existing methods that often require normalization performed beforehand, RCRdiff directly handles raw read counts and jointly models the behaviors of different types of internal controls along with DE and non-DE gene patterns. D

SUBMITTER: Xu C 

PROVIDER: S-EPMC8795478 | biostudies-literature | 2022 Feb

REPOSITORIES: biostudies-literature