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

Functions

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

Files

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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