Volcano plots in analyzing differential expressions with mRNA microarrays

J Bioinform Comput Biol. 2012 Dec;10(6):1231003. doi: 10.1142/S0219720012310038. Epub 2012 Oct 15.

Abstract

A volcano plot displays unstandardized signal (e.g. log-fold-change) against noise-adjusted/standardized signal (e.g. t-statistic or -log(10)(p-value) from the t-test). We review the basic and interactive use of the volcano plot and its crucial role in understanding the regularized t-statistic. The joint filtering gene selection criterion based on regularized statistics has a curved discriminant line in the volcano plot, as compared to the two perpendicular lines for the "double filtering" criterion. This review attempts to provide a unifying framework for discussions on alternative measures of differential expression, improved methods for estimating variance, and visual display of a microarray analysis result. We also discuss the possibility of applying volcano plots to other fields beyond microarray.

Publication types

  • Review

MeSH terms

  • Animals
  • Gene Expression Profiling / methods
  • Humans
  • Models, Statistical*
  • Oligonucleotide Array Sequence Analysis / methods*
  • Oligonucleotide Array Sequence Analysis / statistics & numerical data
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism*
  • Software

Substances

  • RNA, Messenger