acde: Artificial Components Detection of Differentially Expressed Genes

This package provides a multivariate inferential analysis method for detecting differentially expressed genes in gene expression data. It uses artificial components, close to the data's principal components but with an exact interpretation in terms of differential genetic expression, to identify differentially expressed genes while controlling the false discovery rate (FDR). The methods on this package are described in the vignette or in the article 'Multivariate Method for Inferential Identification of Differentially Expressed Genes in Gene Expression Experiments' by J. P. Acosta, L. Lopez-Kleine and S. Restrepo (2015, pending publication).

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("acde")
AuthorJuan Pablo Acosta, Liliana Lopez-Kleine
Bioconductor views DifferentialExpression GeneExpression Microarray PrincipalComponent TimeCourse mRNAMicroarray
Date of publicationNone
MaintainerJuan Pablo Acosta <jpacostar@unal.edu.co>
LicenseGPL-3
Version1.6.0

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/ac.R R/ac2.R R/bcaFDR.R R/fdr.R R/plot.STP.R R/plot.TC.R R/print.STP.R R/print.TC.R R/qval.R R/stp.R R/summary.TC.R R/tc.R
build
build/vignette.rds
data
data/datalist
data/phytophthora.rda
inst
inst/CITATION
inst/doc
inst/doc/acde.R
inst/doc/acde.Rnw
inst/doc/acde.pdf
inst/unitTests
inst/unitTests/test_acde.R
man
man/ac.Rd man/acde-package.Rd man/bcaFDR.Rd man/fdr.Rd man/phytophthora.Rd man/plot.STP.Rd man/plot.TC.Rd man/print.STP.Rd man/print.TC.Rd man/qval.Rd man/stp.Rd man/tc.Rd
tests
tests/runTests.R
vignettes
vignettes/Plot_PI_7.pdf
vignettes/acde.Rnw
vignettes/acde.bib
vignettes/resVignette.rda

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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