# Multiple Testing using SAM and Efron's Empirical Bayes Approaches

## Documentation for package ‘siggenes’ version 1.58.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

args.ebam | Help files or argument list for EBAM-specific methods
args.finda0 | Help files or argument list for FindA0-specific methods
args.sam | Help files or argument list for SAM-specific methods
cat.ebam | EBAM Analysis for Categorical Data
cat.stat | SAM Analysis for Categorical Data
chisq.ebam | EBAM Analysis for Categorical Data
chisq.stat | SAM Analysis for Categorical Data
d.stat | SAM Analysis Using a Modified t-statistic
delta.plot | Delta Plots
denspr | Density Estimation
EBAM | Class EBAM
ebam | Empirical Bayes Analysis of Microarrays
EBAM-class | Class EBAM
ebam2excel | CSV file of a SAM or an EBAM object
ebam2html | HTML page for a SAM or an EBAM object
ebamControl | Further EBAM Arguments
find.a0 | Computation of the Fudge Factor
find.a0Control | Further EBAM Arguments
FindA0 | Class FindA0
FindA0-class | Class FindA0
findDelta | Finding the Threshold Delta
fudge2 | Fudge Factor
fuzzy.ebam | EBAM and SAM for Fuzzy Genotype Calls
fuzzy.stat | 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
identify-method | Class SAM
limma2ebam | limma to SAM or EBAM
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
plot-method | Class EBAM
plot-method | Class FindA0
plot-method | Class SAM
plotArguments | Plot Arguments
plotFindArguments | Plot Arguments
print-method | Class EBAM
print-method | Class FindA0
print-method | Class SAM
print-method | Classes sumSAM and sumEBAM
qvalue.cal | Computation of the q-value
rowRanksWilc | Rowwise Wilcoxon Rank Sum Statistics
rowWilcoxon | Rowwise Wilcoxon Rank Sum Statistics
SAM | Class SAM
sam | Significance Analysis of Microarray
SAM-class | Class SAM
sam.plot2 | SAM Plot
sam2excel | CSV file of a SAM or an EBAM object
sam2html | HTML page for a SAM or an EBAM object
samControl | Further SAM Arguments
show-method | Class EBAM
show-method | Class FindA0
show-method | Class SAM
show-method | Classes sumSAM and sumEBAM
siggenes2excel | CSV file of a SAM or an EBAM object
siggenes2html | HTML page for a SAM or an EBAM object
sumEBAM-class | Classes sumSAM and sumEBAM
summary-method | Class EBAM
summary-method | Class SAM
sumSAM-class | Classes sumSAM and sumEBAM
trend.ebam | EBAM Analysis of Linear Trend
trend.ebam.data.frame | EBAM Analysis of Linear Trend
trend.ebam.default | EBAM Analysis of Linear Trend
trend.ebam.list | EBAM Analysis of Linear Trend
trend.stat | SAM Analysis of Linear Trend
trend.stat.data.frame | SAM Analysis of Linear Trend
trend.stat.default | SAM Analysis of Linear Trend
trend.stat.list | 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
z.find | EBAM analysis Using t- or F-test