DEDS: Differential Expression via Distance Summary for Microarray Data
Version 1.50.0

This library contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F statistics and B statistics. It also implements a new methodology called DEDS (Differential Expression via Distance Summary), which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach.

Browse man pages Browse package API and functions Browse package files

AuthorYuanyuan Xiao <yxiao@itsa.ucsf.edu>, Jean Yee Hwa Yang <jeany@maths.usyd.edu.au>.
Bioconductor views DifferentialExpression Microarray
Date of publicationNone
MaintainerYuanyuan Xiao <yxiao@itsa.ucsf.edu>
LicenseLGPL
Version1.50.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("DEDS")

Man pages

affySpikeIn: Gene expression dataset from Affymetrix Spike-in Experiments
aggregateFun: Aggregate Statistical Functions for DEDS
ApoA1: Gene expression dataset from the ApoA1 Experiment
comp.adjp: Computing permutation based step-down maxT adjusted p values...
comp.B: Computing B-statistics for Differential Expression
comp.ebayes: Computing Empirical Bayes Statistics for Differential...
comp.F: Computing F-statistic for Differential Expression
comp.FC: Computing Fold Change for Differential Expression
comp.fdr: Computing permutation based q values controlling false...
comp.modF: Computing Moderated t-statistics for Differential Expression
comp.modt: Computing Moderated t-statistics for Differential Expression
comp.SAM: Computing SAM Statistics for Differential Expression
comp.stat: Computing Test Statistics for Differential Expression
comp.t: Computing One and Two Sample t-statistic for Differential...
comp.unadjp: Computing permutation based unadjusted p values for each row...
deds.chooseTest: Selection of the Most Common Statistics for Differential...
deds.class: DEDS Result List - class
deds.genExtra: Generating Extra Parameters for Test Statistics Functions for...
DEDS-internal: Internal DEDS functions
deds.pval: Differential Expression via Distance Summary of p Values from...
deds.stat: Differential Expression via Distance Summary of Multiple...
deds.stat.linkC: Differentail Expression via Distance Summary of Multiple...
hist.DEDS: Histogram for DEDS Objects
pairs.DEDS: Pairs Plot for DEDS Objects
qqnorm.DEDS: Normal Q-Q Plot for DEDS Objects
topgenes: Table of Top Genes from DEDS

Functions

ApoA1 Man page
ApoA1.L Man page
DEDS Man page
DEDS-class Man page
affySpikeIn Man page
affySpikeIn.L Man page
affySpikeIn.gnames Man page
aggregateFun Man page Source code
comp.B Man page Source code
comp.F Man page Source code
comp.FC Man page Source code
comp.SAM Man page Source code
comp.adjp Man page Source code
comp.ebayes Man page Source code
comp.fdr Man page Source code
comp.modF Man page Source code
comp.modt Man page Source code
comp.stat Man page Source code
comp.t Man page Source code
comp.unadjp Man page Source code
deds.calcAdjP Man page Source code
deds.calcFDR Man page Source code
deds.checkB Man page Source code
deds.checkX Man page Source code
deds.checkclasslabel Man page Source code
deds.checkothers Man page Source code
deds.chooseTest Man page Source code
deds.genExtra Man page Source code
deds.next.sample Man page Source code
deds.pval Man page Source code
deds.stat Man page Source code
deds.stat.linkC Man page Source code
euclidean Man page Source code
hist Man page
hist-methods Man page
hist.DEDS Man page Source code
pairs Man page
pairs-methods Man page
pairs.DEDS Man page Source code
qqnorm Man page
qqnorm-methods Man page
qqnorm.DEDS Man page Source code
sam.fdr Man page Source code
sam.multiclass.func Man page Source code
sam.oneclass.func Man page Source code
sam.s0 Man page Source code
sam.twoclass.func Man page Source code
spikedgene Man page
test.checkX Man page Source code
topgenes Man page Source code
type2test Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/DEDS.R
build
build/vignette.rds
data
data/ApoA1.RData
data/affySpikeIn.RData
data/datalist
inst
inst/doc
inst/doc/DEDS.R
inst/doc/DEDS.pdf
inst/doc/DEDS.rnw
man
man/ApoA1.Rd
man/DEDS-internal.Rd
man/affySpikeIn.Rd
man/aggregateFun.Rd
man/comp.B.Rd
man/comp.F.Rd
man/comp.FC.Rd
man/comp.SAM.Rd
man/comp.adjp.Rd
man/comp.ebayes.Rd
man/comp.fdr.Rd
man/comp.modF.Rd
man/comp.modt.Rd
man/comp.stat.Rd
man/comp.t.Rd
man/comp.unadjp.Rd
man/deds.chooseTest.Rd
man/deds.class.Rd
man/deds.genExtra.Rd
man/deds.pval.Rd
man/deds.stat.Rd
man/deds.stat.linkC.Rd
man/hist.DEDS.Rd
man/pairs.DEDS.Rd
man/qqnorm.DEDS.Rd
man/topgenes.Rd
src
src/deds.c
src/distance.c
src/input.c
src/manip.c
src/random.c
src/sampling.c
src/stat_fun.c
src/utilities.h
vignettes
vignettes/DEDS.rnw
DEDS documentation built on May 20, 2017, 10:17 p.m.