Volcano plots in analyzing differential expressions with mRNA microarrays

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...

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Bibliographic Details
Published in:Journal of bioinformatics and computational biology Vol. 10; no. 6; p. 1231003
Main Author: Li, Wentian
Format: Journal Article
Language:English
Published: Singapore 01.12.2012
Subjects:
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
ISSN:1757-6334, 1757-6334
Online Access:Get more information
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Summary: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.
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ISSN:1757-6334
1757-6334
DOI:10.1142/S0219720012310038