Voom: Precision Weights Unlock Linear Model Analysis Tools for RNA-seq Read Counts

Genome Biol. 2014 Feb 3;15(2):R29. doi: 10.1186/gb-2014-15-2-r29.

Abstract

New normal linear modeling strategies are presented for analyzing read counts from RNA-seq experiments. The voom method estimates the mean-variance relationship of the log-counts, generates a precision weight for each observation and enters these into the limma empirical Bayes analysis pipeline. This opens access for RNA-seq analysts to a large body of methodology developed for microarrays. Simulation studies show that voom performs as well or better than count-based RNA-seq methods even when the data are generated according to the assumptions of the earlier methods. Two case studies illustrate the use of linear modeling and gene set testing methods.

MeSH terms

  • Algorithms*
  • Base Sequence
  • Bayes Theorem
  • Computer Simulation
  • Gene Expression Profiling
  • High-Throughput Nucleotide Sequencing / methods*
  • Linear Models*
  • RNA / genetics*
  • Sequence Analysis, RNA

Substances

  • RNA