DEDS: Differential Expression via Distance Summary for Microarray Data

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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.

Author
Yuanyuan Xiao <yxiao@itsa.ucsf.edu>, Jean Yee Hwa Yang <jeany@maths.usyd.edu.au>.
Date of publication
None
Maintainer
Yuanyuan Xiao <yxiao@itsa.ucsf.edu>
License
LGPL
Version
1.48.0

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