Nicolas Servant, Eleonore Gravier, Pierre Gestraud, Cecile
Laurent, Caroline Paccard, Anne Biton, Jonas Mandel, Bernard
Asselain, Emmanuel Barillot, Philippe Hupe
R (>= 2.10), cluster, heatmap.plus, FactoMineR, GOstats,
survival, multtest, gcrma, GSA, siggenes, MASS, biomaRt,
xtable, AnnotationDbi

Nicolas Servant, Eleonore Gravier, Pierre Gestraud, Cecile Laurent, Caroline Paccard, Anne Biton, Jonas Mandel, Bernard Asselain, Emmanuel Barillot, Philippe Hupe
We propose both a clear analysis strategy and a selection of tools to investigate microarray gene expression data. The most usual and relevant existing R functions were discussed, validated and gathered in an easy-to-use R package (EMA) devoted to gene expression microarray analysis. These functions were improved for ease of use, enhanced visualisation and better interpretation of results.

siggenes, affy, multtest, survival, xtable, gcrma,
heatmap.plus, biomaRt, GSA, MASS, FactoMineR, cluster
hgu133plus2.db, lumi, vsn, GOstats, GO.db

siggenes, affy, multtest, survival, xtable, gcrma,
heatmap.plus, biomaRt, GSA, MASS, FactoMineR, cluster,
AnnotationDbi

siggenes, affy, multtest, survival, xtable, gcrma,
heatmap.plus, biomaRt, GSA, MASS, FactoMineR, cluster,
AnnotationDbi, Biobase
hgu133plus2.db, lumi, GOstats, Category, vsn,GO.db,
BiocGenerics, GSEABase

c(person(given = "Xiuquan",
family = "Nie",
role = c("aut", "cph", "cre"),
email = "niexiuquan1995@foxmail.com"),
person(given = "Mengyi",
family = "Wang",
role = c("ctb", "rev")),
person(given = "Weihong",
family = "Chen",
role = c("fnd")))
Xiuquan Nie [aut, cph, cre],
Mengyi Wang [ctb, rev],
Weihong Chen [fnd]
DNA methylation is essential for human, and environment can change the DNA methylation
and affect body status. Epigenome-Wide Mediation Analysis Study (EMAS) can find
potential mediator CpG sites between exposure (x) and outcome (y) in epigenome-wide.
For more information on the methods we used, please see the following references:
Tingley, D. (2014) <doi:10.18637/jss.v059.i05>,
Turner, S. D. (2018) <doi:10.21105/joss.00731>.