Differential Expression via Distance Summary for Microarray Data

Documentation for package ‘DEDS’ version 1.26.0

DESCRIPTION file.
Overview of user guides and package vignettes; browse directory.

Help Pages

affySpikeIn	Gene expression dataset from Affymetrix Spike-in Experiments
affySpikeIn.gnames	Gene expression dataset from Affymetrix Spike-in Experiments
affySpikeIn.L	Gene expression dataset from Affymetrix Spike-in Experiments
aggregateFun	Aggregate Statistical Functions for DEDS
ApoA1	Gene expression dataset from the ApoA1 Experiment
ApoA1.L	Gene expression dataset from the ApoA1 Experiment
comp.adjp	Computing permutation based step-down maxT adjusted p values for each row of a matrix
comp.B	Computing B-statistics for Differential Expression
comp.ebayes	Computing Empirical Bayes Statistics for Differential Expression
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 discovery rate for each row of a matrix
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 Expression
comp.unadjp	Computing permutation based unadjusted p values for each row of a matrix
DEDS	DEDS Result List - class
DEDS-class	DEDS Result List - class
deds.chooseTest	Selection of the Most Common Statistics for Differential Expression
deds.genExtra	Generating Extra Parameters for Test Statistics Functions for Differential Expression
deds.pval	Differential Expression via Distance Summary of p Values from Multiple Models
deds.stat	Differential Expression via Distance Summary of Multiple Statistics
deds.stat.linkC	Differentail Expression via Distance Summary of Multiple Statistics
hist	Histogram for DEDS Objects
hist-methods	Histogram for DEDS Objects
hist.DEDS	Histogram for DEDS Objects
pairs	Pairs Plot for DEDS Objects
pairs-methods	Pairs Plot for DEDS Objects
pairs.DEDS	Pairs Plot for DEDS Objects
qqnorm	Normal Q-Q Plot for DEDS Objects
qqnorm-methods	Normal Q-Q Plot for DEDS Objects
qqnorm.DEDS	Normal Q-Q Plot for DEDS Objects
spikedgene	Gene expression dataset from Affymetrix Spike-in Experiments
topgenes	Table of Top Genes from DEDS