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

Files in this package

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.

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