# Differential Expression via Distance Summary for Microarray Data

## Documentation for package ‘DEDS’ version 1.12.1

## User Guides and Package Vignettes

Read overview or browse directory.

## Help 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 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 | Differentail 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