title: Normalizing RNA-sequencing data by modeling hidden covariates with prior knowledge.
abstract: Transcriptomic assays that measure expression levels are widely used to study the manifestation of environmental or genetic variations in cellular processes. RNA-sequencing in particular has the potential to considerably improve such understanding because of its capacity to assay the entire transcriptome, including novel transcriptional events. However, as with earlier expression assays, analysis of RNA-sequencing data requires carefully accounting for factors that may introduce systematic, confounding variability in the expression measurements, resulting in spurious correlations. Here, we consider the problem of modeling and removing the effects of known and hidden confounding factors from RNA-sequencing data. We describe a unified residual framework that encapsulates existing approaches, and using this framework, present a novel method, HCP (Hidden Covariates with Prior). HCP uses a more informed assumption about the confounding factors, and performs as well or better than existing approaches while having a much lower computational cost. Our experiments demonstrate that accounting for known and hidden factors with appropriate models improves the quality of RNA-sequencing data in two very different tasks: detecting genetic variations that are associated with nearby expression variations (cis-eQTLs), and constructing accurate co-expression networks.
authors.affiliation: Department of Computer Science, Stanford University, Stanford, California, USA.
authors.forename: Sara
authors.initials: S
authors.lastname: Mostafavi
authors.forename: Alexis
authors.initials: A
authors.lastname: Battle
authors.forename: Xiaowei
authors.initials: X
authors.lastname: Zhu
authors.forename: Alexander E
authors.initials: AE
authors.lastname: Urban
authors.forename: Douglas
authors.initials: D
authors.lastname: Levinson
authors.forename: Stephen B
authors.initials: SB
authors.lastname: Montgomery
authors.forename: Daphne
authors.initials: D
authors.lastname: Koller
mesh_terms: D001483:Base Sequence / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D008957:Models, Genetic; D012107:Research Design; D017423:Sequence Analysis, RNA / Q000379:methods* / Q000592:standards; D059467:Transcriptome / Q000235:genetics*