Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses

Liu, R; Holik, AZ; Su, S; Jansz, N; Chen, K; Leong, HS; Blewitt, ME; Asselin-Labat, ML; Smyth, GK; Ritchie, ME

Author(s): Liu, R; Holik, AZ; Su, S; Jansz, N; Chen, K; Leong, HS; Blewitt, ME; Asselin-Labat, ML; Smyth, GK; Ritchie, ME;
Details: Publication Year 2015-04-29,Volume 43,Issue #15,Page e97
Journal Title: Nucleic Acids Res
Publication Type: Journal Article
Abstract: Variations in sample quality are frequently encountered in small RNA-sequencing experiments, and pose a major challenge in a differential expression analysis. Removal of high variation samples reduces noise, but at a cost of reducing power, thus limiting our ability to detect biologically meaningful changes. Similarly, retaining these samples in the analysis may not reveal any statistically significant changes due to the higher noise level. A compromise is to use all available data, but to down-weight the observations from more variable samples. We describe a statistical approach that facilitates this by modelling heterogeneity at both the sample and observational levels as part of the differential expression analysis. At the sample level this is achieved by fitting a log-linear variance model that includes common sample-specific or group-specific parameters that are shared between genes. The estimated sample variance factors are then converted to weights and combined with observational level weights obtained from the mean-variance relationship of the log-counts-per-million using 'voom'. A comprehensive analysis involving both simulations and experimental RNA-sequencing data demonstrates that this strategy leads to a universally more powerful analysis and fewer false discoveries when compared to conventional approaches. This methodology has wide application and is implemented in the open-source 'limma' package.
Publisher: OUP
Research Division(s): Molecular Medicine; Stem Cells And Cancer; Bioinformatics
PubMed ID: 25925576
Publisher's Version: https://doi.org/10.1093/nar/gkv412
Open Access at Publisher's Site: http://nar.oxfordjournals.org/content/early/2015/04/28/nar.gkv412.long
NHMRC Grants: NHMRC/1050661, NHMRC/1045936,
Terms of Use/Rights Notice: Refer to copyright notice on published article.

Creation Date: 2015-05-21 10:20:31

Last Modified: 2015-09-11 09:54:17