Moderated statistical tests for assessing differences in tag abundance

Robinson, MD; Smyth, GK

Author(s): Robinson, MD; Smyth, GK;
Details: Publication Year 2007-11-01,Volume 23,Issue #21,Page 2881-2887
Journal Title: BIOINFORMATICS
Publication Type: Journal Article
Abstract: Motivation: Digital gene expression (DGE) technologies measure gene expression by counting sequence tags. They are sensitive technologies for measuring gene expression on a genomic scale, without the need for prior knowledge of the genome sequence. As the cost of sequencing DNA decreases, the number of DGE datasets is expected to grow dramatically. Various tests of differential expression have been proposed for replicated DGE data using binomial, Poisson, negative binomial or pseudo-likelihood (PL) models for the counts, but none of the these are usable when the number of replicates is very small. Results: We develop tests using the negative binomial distribution to model overdispersion relative to the Poisson, and use conditional weighted likelihood to moderate the level of overdispersion across genes. Not only is our strategy applicable even with the smallest number of libraries, but it also proves to be more powerful than previous strategies when more libraries are available. The methodology is equally applicable to other counting technologies, such as proteomic spectral counts.
Publisher: OXFORD UNIV PRESS
Keywords: GENE-EXPRESSION PROFILES; SERIAL ANALYSIS; BAYESIAN-INFERENCE; SAGE DATA; CANCERS; CELLS
Publisher's Version: https://doi.org/10.1093/bioinformatics/btm453
Terms of Use/Rights Notice: Refer to copyright notice on published article.

Creation Date: 2007-11-01 12:00:00