DEDS: Differential Expression via Distance Summary for Microarray Data

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.

AuthorYuanyuan Xiao <yxiao@itsa.ucsf.edu>, Jean Yee Hwa Yang <jeany@maths.usyd.edu.au>.
Date of publicationNone
MaintainerYuanyuan Xiao <yxiao@itsa.ucsf.edu>
LicenseLGPL
Version1.48.0

View on Bioconductor

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

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

Files

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

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

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.