siggenes: Multiple testing using SAM and Efron's empirical Bayes approaches
Version 1.50.0

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).

Browse man pages Browse package API and functions Browse package files

AuthorHolger Schwender
Bioconductor views DifferentialExpression ExonArray GeneExpression Microarray MultipleComparison SNP
Date of publicationNone
MaintainerHolger Schwender <holger.schw@gmx.de>
LicenseLGPL (>= 2)
Version1.50.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("siggenes")

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

Functions

EBAM Man page
EBAM-class Man page
FindA0 Man page
FindA0-class Man page
Rfold.cal Man page Source code
SAM Man page
SAM-class Man page
add.target2href Man page Source code
adjust.for.mt Man page Source code
args.ebam Man page
args.finda0 Man page
args.sam Man page Source code
build.dperm Man page Source code
cat.ebam Man page Source code
cat.null Man page
cat.null.approx Man page
cat.null.approx2 Man page Source code
cat.stat Man page Source code
check.chipname Man page Source code
checkA0 Man page
checkDBs Source code
checkFUNout Man page
checkInitialDelta Man page
checkQuantiles Man page
chisq.ebam Man page Source code
chisq.stat Man page Source code
chisqClass Man page
chisqClassSplitted Man page Source code
chisqEbamMissing Source code
chisqStatMissing Source code
col2hex Man page Source code
compFailABF Source code
compFailFuzzy Source code
compFailure Man page
compFailureMat2 Man page
compFailureSubset Man page
compFalse Man page
compNumber Man page
compPermStat Man page
compPermTrendStat Source code
compRatio Man page
computeContCols Man page
computeRS Man page
d.null Man page Source code
d.stat Man page Source code
delta.plot Man page Source code
denspr Man page Source code
ebam Man page
ebam2excel Man page
ebam2html Man page Source code
ebamA0 Man page
ebamControl Man page Source code
find.a0 Man page
find.a0Control Man page Source code
findDelta Man page
findFDR Man page
findNumber Man page
finda02html Man page Source code
formatSAM Man page Source code
fudge2 Man page Source code
fuzzy.ebam Man page Source code
fuzzy.null Source code
fuzzy.null.abf Source code
fuzzy.null.approx Source code
fuzzy.stat Man page Source code
getFailure Man page
getQuantiles Man page Source code
getSuccesses Man page
getTD4Affy Man page Source code
getTD4rs Man page Source code
help.ebam Man page
help.finda0 Man page
help.sam Man page Source code
identify,SAM-method Man page
limma2ebam Man page Source code
limma2sam Man page Source code
lines.denspr Source code
link.genes Man page Source code
link.siggenes Man page Source code
list.siggenes Man page
make.tablecode Man page Source code
makeA0mat Man page
md.plot Man page Source code
na.handling Man page Source code
na.replace.cont Man page Source code
nclass.wand Man page Source code
onAttach Source code
pairt.cl.transform Man page Source code
pairt.samp Man page Source code
pairt.samp.transform Man page Source code
pi0.est Man page Source code
pi0.est2 Man page
pi0.est3 Man page
plot,EBAM,ANY-method Man page
plot,EBAM-method Man page
plot,FindA0,ANY-method Man page
plot,FindA0-method Man page
plot,SAM,ANY-method Man page
plot,SAM-method Man page
plot.denspr Source code
plotArguments Man page Source code
plotFindArguments Man page Source code
plotLegendLines Source code
pretty.mat.fdr Man page Source code
pretty.mat.sig Man page Source code
print,EBAM-method Man page
print,FindA0-method Man page
print,SAM-method Man page
print,sumEBAM-method Man page
print,sumSAM-method Man page
quantiles Man page Source code
qvalue.cal Man page Source code
recodeLevel Man page Source code
recodeVal Man page Source code
rowRanksWilc Man page Source code
rowWilcoxon Man page Source code
sam Man page Source code
sam.plot2 Man page Source code
sam2excel Man page
sam2html Man page Source code
samControl Man page Source code
setup.mat.samp Man page Source code
setupMatSamp2 Source code
show,EBAM-method Man page
show,FindA0-method Man page
show,SAM-method Man page
show,sumEBAM-method Man page
show,sumSAM-method Man page
siggenes2excel Man page
siggenes2html Man page Source code
stats.cal Man page Source code
sumEBAM-class Man page
sumSAM-class Man page
summary,EBAM-method Man page
summary,SAM-method Man page
trend.ebam Man page Man page Source code
trend.ebam.data.frame Man page Source code
trend.ebam.default Man page Source code
trend.ebam.list Man page Source code
trend.null Source code
trend.stat Man page Source code
trend.stat.data.frame Man page Source code
trend.stat.default Man page Source code
trend.stat.list Man page Source code
truncZ Man page
wilc.ebam Man page Source code
wilc.stat Man page Source code
z.ebam Man page
z.find Man page

Files

DESCRIPTION
NAMESPACE
R
R/EBAM-class.R
R/FindA0-class.R
R/Rfold.cal.R
R/SAM-class.R
R/add.target2href.R
R/adjust.for.mt.R
R/args.ebam.R
R/args.finda0.R
R/args.sam.R
R/build.dperm.R
R/cat.ebam.R
R/cat.null.R
R/cat.null.approx.R
R/cat.null.approx2.R
R/cat.stat.R
R/check.chipname.R
R/checkA0.R
R/checkDBs.R
R/checkFUNout.R
R/checkInitialDelta.R
R/checkQuantiles.R
R/chisq.ebam.R
R/chisq.stat.R
R/chisqClass.R
R/chisqClassSplitted.R
R/col2hex.R
R/compFailure.R
R/compFailureMat2.R
R/compFailureSubset.R
R/compFalse.R
R/compNumber.R
R/compPermStat.R
R/compRatio.R
R/computeContCols.R
R/computeRS.R
R/d.null.R
R/d.stat.R
R/delta.plot.R
R/denspr.R
R/ebam.R
R/ebam2excel.R
R/ebam2html.R
R/ebamA0.R
R/find.a0.R
R/findDelta.R
R/findFDR.R
R/findNumber.R
R/finda02html.R
R/formatSAM.R
R/fudge2.R
R/fuzzy.ebam.R
R/fuzzy.stat.R
R/getFailure.R
R/getQuantiles.R
R/getSuccesses.R
R/getTD4Affy.R
R/getTD4rs.R
R/help.ebam.R
R/help.finda0.R
R/help.sam.R
R/limma2sam.R
R/link.genes.R
R/link.siggenes.R
R/list.siggenes.R
R/make.tablecode.R
R/makeA0mat.R
R/md.plot.R
R/na.handling.R
R/na.replace.cont.R
R/nclass.wand.R
R/pairt.cl.transform.R
R/pairt.samp.R
R/pairt.samp.transform.R
R/pi0.est.R
R/pi0.est2.R
R/pi0.est3.R
R/plotArguments.R
R/plotFindArguments.R
R/quantiles.R
R/qvalue.cal.R
R/recodeVal.R
R/rowRanksWilc.R
R/rowWilcoxon.R
R/sam.R
R/sam.plot2.R
R/sam2excel.R
R/sam2html.R
R/samControl.R
R/setup.mat.samp.R
R/siggenes2excel.R
R/siggenes2html.R
R/stats.cal.R
R/sumEBAM-class.R
R/sumSAM-class.R
R/trend.ebam.R
R/trend.stat.R
R/truncZ.R
R/wilc.ebam.R
R/wilc.stat.R
R/z.ebam.R
R/z.find.R
R/zzz.R
build
build/vignette.rds
inst
inst/doc
inst/doc/siggenes.R
inst/doc/siggenes.Rnw
inst/doc/siggenes.pdf
man
man/EBAM-class.Rd
man/FindA0-class.Rd
man/SAM-class.Rd
man/chisq.ebam.Rd
man/chisq.stat.Rd
man/d.stat.Rd
man/delta.plot.Rd
man/denspr.Rd
man/ebam.Rd
man/ebamControl.Rd
man/find.a0.Rd
man/findDelta.Rd
man/fudge2.Rd
man/fuzzy.ebam.Rd
man/help.ebam.Rd
man/help.finda0.Rd
man/help.sam.Rd
man/limma2sam.Rd
man/link.genes.Rd
man/link.siggenes.Rd
man/list.siggenes.Rd
man/md.plot.Rd
man/nclass.wand.Rd
man/pi0.est.Rd
man/plotArguments.Rd
man/plotFindArguments.Rd
man/qvalue.cal.Rd
man/rowWilcoxon.Rd
man/sam.Rd
man/sam.plot2.Rd
man/samControl.Rd
man/siggenes-internal.Rd
man/siggenes2excel.Rd
man/siggenes2html.Rd
man/sumSAM-class.Rd
man/trend.ebam.Rd
man/trend.stat.Rd
man/wilc.ebam.Rd
man/wilc.stat.Rd
man/z.ebam.Rd
vignettes
vignettes/ebamplot.eps
vignettes/ebamplot.png
vignettes/finda0.eps
vignettes/finda0.png
vignettes/identify.sam.html
vignettes/plot.ebam.html
vignettes/plot.finda0.html
vignettes/plot.sam.html
vignettes/print.ebam.html
vignettes/print.finda0.html
vignettes/print.sam.html
vignettes/samplot.png
vignettes/samplot.ps
vignettes/siggenes.Rnw
vignettes/siggenesRnews.pdf
vignettes/summary.ebam.html
vignettes/summary.sam.html
siggenes documentation built on May 20, 2017, 10:21 p.m.