Skip to main content
Article thumbnail
Location of Repository

Application of Volcano Plots in Analyses of mRNA Differential Expressions with Microarrays

By Wentian Li

Abstract

Volcano plot displays unstandardized signal (e.g. log-fold-change) against noise-adjusted/standardized signal (e.g. t-statistic or -log10(p-value) from the t test). We review the basic and an 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 an 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 to apply volcano plots to other fields beyond microarray.Comment: 8 figure

Topics: Quantitative Biology - Quantitative Methods, Quantitative Biology - Genomics
Year: 2013
DOI identifier: 10.1142/S0219720012310038
OAI identifier: oai:arXiv.org:1103.3434
Download PDF:
Sorry, we are unable to provide the full text but you may find it at the following location(s):
  • http://arxiv.org/abs/1103.3434 (external link)
  • Suggested articles


    To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.