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).

Author
Holger Schwender
Date of publication
None
Maintainer
Holger Schwender <holger.schw@gmx.de>
License
LGPL (>= 2)
Version
1.48.0

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