Published by the Foundation for Open Access Statistics
Editors-in-chief: Bettina Grün, Torsten Hothorn, Edzer Pebesma, Achim Zeileis    ISSN 1548-7660; CODEN JSSOBK
Factor Analysis for Multiple Testing (FAMT): An R Package for Large-Scale Significance Testing under Dependence | Causeur | Journal of Statistical Software
Authors: David Causeur, Chloe Friguet, Magalie Houee-Bigot, Maela Kloareg
Title: Factor Analysis for Multiple Testing (FAMT): An R Package for Large-Scale Significance Testing under Dependence
Abstract: The R package FAMT (factor analysis for multiple testing) provides a powerful method for large-scale significance testing under dependence. It is especially designed to select differentially expressed genes in microarray data when the correlation structure among gene expressions is strong. Indeed, this method reduces the negative impact of dependence on the multiple testing procedures by modeling the common information shared by all the variables using a factor analysis structure. New test statistics for general linear contrasts are deduced, taking advantage of the common factor structure to reduce correlation and consequently the variance of error rates. Thus, the FAMT method shows improvements with respect to most of the usual methods regarding the non discovery rate and the control of the false discovery rate (FDR).
The steps of this procedure, each of them corresponding to R functions, are illustrated in this paper by two microarray data analyses. We first present how to import the gene ex- pression data, the covariates and gene annotations. The second step includes the choice of the optimal number of factors, the factor model fitting, and provides a list of selected genes according to a preset FDR control level. Finally, diagnostic plots are provided to help the user interpret the factors using available external information on either genes or arrays.

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Paper: Factor Analysis for Multiple Testing (FAMT): An R Package for Large-Scale Significance Testing under Dependence     Download PDF (Downloads: 3753)
Supplements:
FAMT_2.3.tar.gz: R source package Download (Downloads: 548; 3MB)
v40i14.R: R example code from the paper Download (Downloads: 551; 2KB)
Expr.txt: Expression data from second example in ASCII format Download (Downloads: 619; 6MB)
covar.txt: Covariable data from second example in ASCII format Download (Downloads: 606; 386B)

DOI: 10.18637/jss.v040.i14

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Code: GNU General Public License (at least one of version 2 or version 3) or a GPL-compatible license.