Multiple testing using SAM and Efron's empirical Bayes approaches


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Documentation for package ‘siggenes’ version 1.16.0

User Guides and Package Vignettes

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Help Pages

A B C D E F H I L N P Q R S W Z

-- A --

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

-- B --

buildSNPannotation Construct Annotation for Affymetrix SNP Chips

-- C --

cat.ebam EBAM Analysis for Categorical Data
cat.stat SAM Analysis for Categorical Data

-- D --

d.stat SAM Analysis Using a Modified t-statistic
delta.plot Delta Plots
denspr Density Estimation

-- E --

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

-- F --

find.a0 Computation of the Fudge Factor
FindA0 Class FindA0
FindA0-class Class FindA0
findDelta Finding the Threshold Delta
fudge2 Fudge Factor

-- H --

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

-- I --

identify,SAM-method Class SAM

-- L --

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

-- N --

nclass.wand Number of cells in a histogram

-- P --

pi0.est Estimation of the prior probability
plot,EBAM-method Class EBAM
plot,FindA0-method Class FindA0
plot,SAM-method Class SAM
plotArguments Plot Arguments
plotFindArguments Plot Arguments
print,EBAM-method Class EBAM
print,FindA0-method Class FindA0
print,SAM-method Class SAM
print,sumEBAM-method Classes sumSAM and sumEBAM
print,sumSAM-method Classes sumSAM and sumEBAM

-- Q --

qvalue.cal Computation of the q-value

-- R --

rowRanksWilc Rowwise Wilcoxon Rank Sum Statistics
rowWilcoxon Rowwise Wilcoxon Rank Sum Statistics

-- S --

SAM Class SAM
sam Significance Analysis of Microarray
SAM-class Class SAM
sam.dstat SAM Analysis Using a Modified t-statistic
sam.plot2 SAM Plot
sam.snp SAM Analysis for Categorical Data
sam.wilc SAM Analysis Using Wilcoxon Rank Statistics
sam2excel CSV file of a SAM or an EBAM object
sam2html HTML page for a SAM or an EBAM object
shortenGeneDescription Shorten the Gene Description
show,EBAM-method Class EBAM
show,FindA0-method Class FindA0
show,SAM-method Class SAM
show,sumEBAM-method Classes sumSAM and sumEBAM
show,sumSAM-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,EBAM-method Class EBAM
summary,SAM-method Class SAM
sumSAM-class Classes sumSAM and sumEBAM

-- W --

wilc.ebam EBAM Analysis Using Wilcoxon Rank Statistics
wilc.stat SAM Analysis Using Wilcoxon Rank Statistics

-- Z --

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