siggenes: Multiple testing using SAM and Efron's empirical Bayes approaches

Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).

AuthorHolger Schwender
Date of publicationNone
MaintainerHolger Schwender <holger.schw@gmx.de>
LicenseLGPL (>= 2)
Version1.48.0

View on Bioconductor

Man pages

chisq.ebam: EBAM Analysis for Categorical Data

chisq.stat: SAM Analysis for Categorical Data

delta.plot: Delta Plots

denspr: Density Estimation

d.stat: SAM Analysis Using a Modified t-statistic

ebam: Empirical Bayes Analysis of Microarrays

EBAM-class: Class EBAM

ebamControl: Further EBAM Arguments

find.a0: Computation of the Fudge Factor

FindA0-class: Class FindA0

findDelta: Finding the Threshold Delta

fudge2: Fudge Factor

fuzzy.ebam: EBAM and SAM for Fuzzy Genotype Calls

help.ebam: Help files or argument list for EBAM-specific methods

help.finda0: Help files or argument list for FindA0-specific methods

help.sam: Help files or argument list for SAM-specific methods

limma2sam: limma to SAM or EBAM

link.genes: Links for a list of genes

link.siggenes: Links for a SAM or an EBAM object

list.siggenes: List of the significant genes

md.plot: MD Plot

nclass.wand: Number of cells in a histogram

pi0.est: Estimation of the prior probability

plotArguments: Plot Arguments

plotFindArguments: Plot Arguments

qvalue.cal: Computation of the q-value

rowWilcoxon: Rowwise Wilcoxon Rank Sum Statistics

sam: Significance Analysis of Microarray

SAM-class: Class SAM

samControl: Further SAM Arguments

sam.plot2: SAM Plot

siggenes2excel: CSV file of a SAM or an EBAM object

siggenes2html: HTML page for a SAM or an EBAM object

siggenes-internal: Internal siggenes functions

sumSAM-class: Classes sumSAM and sumEBAM

trend.ebam: EBAM Analysis of Linear Trend

trend.stat: SAM Analysis of Linear Trend

wilc.ebam: EBAM Analysis Using Wilcoxon Rank Statistics

wilc.stat: SAM Analysis Using Wilcoxon Rank Statistics

z.ebam: EBAM analysis Using t- or F-test

Files in this package

siggenes/DESCRIPTION
siggenes/NAMESPACE
siggenes/R
siggenes/R/EBAM-class.R siggenes/R/FindA0-class.R siggenes/R/Rfold.cal.R siggenes/R/SAM-class.R siggenes/R/add.target2href.R siggenes/R/adjust.for.mt.R siggenes/R/args.ebam.R siggenes/R/args.finda0.R siggenes/R/args.sam.R siggenes/R/build.dperm.R siggenes/R/cat.ebam.R siggenes/R/cat.null.R siggenes/R/cat.null.approx.R siggenes/R/cat.null.approx2.R siggenes/R/cat.stat.R siggenes/R/check.chipname.R siggenes/R/checkA0.R siggenes/R/checkDBs.R siggenes/R/checkFUNout.R siggenes/R/checkInitialDelta.R siggenes/R/checkQuantiles.R siggenes/R/chisq.ebam.R siggenes/R/chisq.stat.R siggenes/R/chisqClass.R siggenes/R/chisqClassSplitted.R siggenes/R/col2hex.R siggenes/R/compFailure.R siggenes/R/compFailureMat2.R siggenes/R/compFailureSubset.R siggenes/R/compFalse.R siggenes/R/compNumber.R siggenes/R/compPermStat.R siggenes/R/compRatio.R siggenes/R/computeContCols.R siggenes/R/computeRS.R siggenes/R/d.null.R siggenes/R/d.stat.R siggenes/R/delta.plot.R siggenes/R/denspr.R siggenes/R/ebam.R siggenes/R/ebam2excel.R siggenes/R/ebam2html.R siggenes/R/ebamA0.R siggenes/R/find.a0.R siggenes/R/findDelta.R siggenes/R/findFDR.R siggenes/R/findNumber.R siggenes/R/finda02html.R siggenes/R/formatSAM.R siggenes/R/fudge2.R siggenes/R/fuzzy.ebam.R siggenes/R/fuzzy.stat.R siggenes/R/getFailure.R siggenes/R/getQuantiles.R siggenes/R/getSuccesses.R siggenes/R/getTD4Affy.R siggenes/R/getTD4rs.R siggenes/R/help.ebam.R siggenes/R/help.finda0.R siggenes/R/help.sam.R siggenes/R/limma2sam.R siggenes/R/link.genes.R siggenes/R/link.siggenes.R siggenes/R/list.siggenes.R siggenes/R/make.tablecode.R siggenes/R/makeA0mat.R siggenes/R/md.plot.R siggenes/R/na.handling.R siggenes/R/na.replace.cont.R siggenes/R/nclass.wand.R siggenes/R/pairt.cl.transform.R siggenes/R/pairt.samp.R siggenes/R/pairt.samp.transform.R siggenes/R/pi0.est.R siggenes/R/pi0.est2.R siggenes/R/pi0.est3.R siggenes/R/plotArguments.R siggenes/R/plotFindArguments.R siggenes/R/quantiles.R siggenes/R/qvalue.cal.R siggenes/R/recodeVal.R siggenes/R/rowRanksWilc.R siggenes/R/rowWilcoxon.R siggenes/R/sam.R siggenes/R/sam.plot2.R siggenes/R/sam2excel.R siggenes/R/sam2html.R siggenes/R/samControl.R siggenes/R/setup.mat.samp.R siggenes/R/siggenes2excel.R siggenes/R/siggenes2html.R siggenes/R/stats.cal.R siggenes/R/sumEBAM-class.R siggenes/R/sumSAM-class.R siggenes/R/trend.ebam.R siggenes/R/trend.stat.R siggenes/R/truncZ.R siggenes/R/wilc.ebam.R siggenes/R/wilc.stat.R siggenes/R/z.ebam.R siggenes/R/z.find.R siggenes/R/zzz.R
siggenes/build
siggenes/build/vignette.rds
siggenes/inst
siggenes/inst/doc
siggenes/inst/doc/siggenes.R
siggenes/inst/doc/siggenes.Rnw
siggenes/inst/doc/siggenes.pdf
siggenes/man
siggenes/man/EBAM-class.Rd siggenes/man/FindA0-class.Rd siggenes/man/SAM-class.Rd siggenes/man/chisq.ebam.Rd siggenes/man/chisq.stat.Rd siggenes/man/d.stat.Rd siggenes/man/delta.plot.Rd siggenes/man/denspr.Rd siggenes/man/ebam.Rd siggenes/man/ebamControl.Rd siggenes/man/find.a0.Rd siggenes/man/findDelta.Rd siggenes/man/fudge2.Rd siggenes/man/fuzzy.ebam.Rd siggenes/man/help.ebam.Rd siggenes/man/help.finda0.Rd siggenes/man/help.sam.Rd siggenes/man/limma2sam.Rd siggenes/man/link.genes.Rd siggenes/man/link.siggenes.Rd siggenes/man/list.siggenes.Rd siggenes/man/md.plot.Rd siggenes/man/nclass.wand.Rd siggenes/man/pi0.est.Rd siggenes/man/plotArguments.Rd siggenes/man/plotFindArguments.Rd siggenes/man/qvalue.cal.Rd siggenes/man/rowWilcoxon.Rd siggenes/man/sam.Rd siggenes/man/sam.plot2.Rd siggenes/man/samControl.Rd siggenes/man/siggenes-internal.Rd siggenes/man/siggenes2excel.Rd siggenes/man/siggenes2html.Rd siggenes/man/sumSAM-class.Rd siggenes/man/trend.ebam.Rd siggenes/man/trend.stat.Rd siggenes/man/wilc.ebam.Rd siggenes/man/wilc.stat.Rd siggenes/man/z.ebam.Rd
siggenes/vignettes
siggenes/vignettes/ebamplot.eps
siggenes/vignettes/ebamplot.png
siggenes/vignettes/finda0.eps
siggenes/vignettes/finda0.png
siggenes/vignettes/identify.sam.html
siggenes/vignettes/plot.ebam.html
siggenes/vignettes/plot.finda0.html
siggenes/vignettes/plot.sam.html
siggenes/vignettes/print.ebam.html
siggenes/vignettes/print.finda0.html
siggenes/vignettes/print.sam.html
siggenes/vignettes/samplot.png
siggenes/vignettes/samplot.ps
siggenes/vignettes/siggenes.Rnw
siggenes/vignettes/siggenesRnews.pdf
siggenes/vignettes/summary.ebam.html
siggenes/vignettes/summary.sam.html

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