Entry: EBAM-class
Aliases: EBAM-class EBAM show,EBAM-method print,EBAM-method plot,EBAM-method summary,EBAM-method
Keywords: classes
Description: Class EBAM
URL: ../../../library/siggenes/html/EBAM-class.html

Entry: FindA0class
Aliases: FindA0-class FindA0 show,FindA0-method print,FindA0-method plot,FindA0-method
Keywords: classes
Description: Class FindA0
URL: ../../../library/siggenes/html/FindA0-class.html

Entry: SAM-class
Aliases: SAM-class SAM identify,SAM-method plot,SAM-method print,SAM-method show,SAM-method summary,SAM-method
Keywords: classes
Description: Class SAM
URL: ../../../library/siggenes/html/SAM-class.html

Entry: buildSNPannotation
Aliases: buildSNPannotation
Keywords: misc
Description: Construct Annotation for Affymetrix SNP Chips
URL: ../../../library/siggenes/html/buildSNPannotation.html

Entry: cat.ebam
Aliases: cat.ebam
Keywords: htest
Description: EBAM Analysis for Categorical Data
URL: ../../../library/siggenes/html/cat.ebam.html

Entry: cat.stat
Aliases: sam.snp cat.stat
Keywords: htest
Description: SAM Analysis for Categorical Data
URL: ../../../library/siggenes/html/cat.stat.html

Entry: d.stat
Aliases: d.stat sam.dstat
Keywords: htest
Description: SAM Analysis Using a Modified t-statistic
URL: ../../../library/siggenes/html/d.stat.html

Entry: delta.plot
Aliases: delta.plot
Keywords: hplot
Description: Delta Plots
URL: ../../../library/siggenes/html/delta.plot.html

Entry: denspr
Aliases: denspr
Keywords: smooth
Description: Density Estimation
URL: ../../../library/siggenes/html/denspr.html

Entry: ebam
Aliases: ebam
Keywords: htest
Description: Empirical Bayes Analysis of Microarrays
URL: ../../../library/siggenes/html/ebam.html

Entry: find.a0
Aliases: find.a0
Keywords: htest
Description: Computation of the Fudge Factor
URL: ../../../library/siggenes/html/find.a0.html

Entry: findDelta
Aliases: findDelta
Keywords: htest
Description: Finding the Threshold Delta
URL: ../../../library/siggenes/html/findDelta.html

Entry: fudge2
Aliases: fudge2
Keywords: optimize
Description: Fudge Factor
URL: ../../../library/siggenes/html/fudge2.html

Entry: help.ebam
Aliases: help.ebam args.ebam
Keywords: documentation
Description: Help files or argument list for EBAM-specific methods
URL: ../../../library/siggenes/html/help.ebam.html

Entry: help.finda0
Aliases: help.finda0 args.finda0
Keywords: documentation
Description: Help files or argument list for FindA0-specific methods
URL: ../../../library/siggenes/html/help.finda0.html

Entry: help.sam
Aliases: help.sam args.sam
Keywords: documentation
Description: Help files or argument list for SAM-specific methods
URL: ../../../library/siggenes/html/help.sam.html

Entry: link.genes
Aliases: link.genes
Keywords: IO file
Description: Links for a list of genes
URL: ../../../library/siggenes/html/link.genes.html

Entry: link.siggenes
Aliases: link.siggenes
Keywords: IO file
Description: Links for a SAM or an EBAM object
URL: ../../../library/siggenes/html/link.siggenes.html

Entry: list.siggenes
Aliases: list.siggenes
Keywords: IO file
Description: List of the significant genes
URL: ../../../library/siggenes/html/list.siggenes.html

Entry: nclass.wand
Aliases: nclass.wand
Keywords: utilities
Description: Number of cells in a histogram
URL: ../../../library/siggenes/html/nclass.wand.html

Entry: pi0.est
Aliases: pi0.est
Keywords: htest smooth
Description: Estimation of the prior probability
URL: ../../../library/siggenes/html/pi0.est.html

Entry: plotArguments
Aliases: plotArguments
Keywords: hplot
Description: Plot Arguments
URL: ../../../library/siggenes/html/plotArguments.html

Entry: plotFindArguments
Aliases: plotFindArguments
Keywords: hplot
Description: Plot Arguments
URL: ../../../library/siggenes/html/plotFindArguments.html

Entry: qvalue.cal
Aliases: qvalue.cal
Keywords: htest
Description: Computation of the q-value
URL: ../../../library/siggenes/html/qvalue.cal.html

Entry: rowWilcoxon
Aliases: rowWilcoxon rowRanksWilc
Keywords: htest
Description: Rowwise Wilcoxon Rank Sum Statistics
URL: ../../../library/siggenes/html/rowWilcoxon.html

Entry: sam
Aliases: sam
Keywords: htest
Description: Significance Analysis of Microarray
URL: ../../../library/siggenes/html/sam.html

Entry: sam.plot2
Aliases: sam.plot2
Keywords: hplot
Description: SAM Plot
URL: ../../../library/siggenes/html/sam.plot2.html

Entry: shortenGeneDescription
Aliases: shortenGeneDescription
Keywords: utilities
Description: Shorten the Gene Description
URL: ../../../library/siggenes/html/shortenGeneDescription.html

Entry: siggenes-internal
Aliases: adjust.for.mt build.dperm d.null pairt.cl.transform pairt.samp pairt.samp.transform Rfold.cal setup.mat.samp stats.cal quantiles add.target2href check.chipname col2hex getTD4Affy make.tablecode pretty.mat.fdr formatSAM pretty.mat.sig filterALL compPermStat cat.null cat.null.approx chisqClass computeContCols checkA0 checkFUNout checkQuantiles compFailure compFailureMat2 compFailureSubset compFalse compNumber compRatio computeRS ebamA0 getFailure getSuccesses makeA0mat pi0.est2 pi0.est3 truncZ finda02html cat.null.approx2 na.handling na.replace.cont getQuantiles recodeVal recodeLevel getTD4rs findFDR findNumber checkInitialDelta chisqClassSplitted
Keywords: internal
Description: Internal siggenes functions
URL: ../../../library/siggenes/html/siggenes-internal.html

Entry: siggenes2excel
Aliases: sam2excel ebam2excel siggenes2excel
Keywords: IO file
Description: CSV file of a SAM or an EBAM object
URL: ../../../library/siggenes/html/siggenes2excel.html

Entry: siggenes2html
Aliases: sam2html ebam2html siggenes2html
Keywords: IO file
Description: HTML page for a SAM or an EBAM object
URL: ../../../library/siggenes/html/siggenes2html.html

Entry: sumSAM-class
Aliases: sumSAM-class print,sumSAM-method show,sumSAM-method sumEBAM-class print,sumEBAM-method show,sumEBAM-method
Keywords: classes
Description: Classes sumSAM and sumEBAM
URL: ../../../library/siggenes/html/sumSAM-class.html

Entry: wilc.ebam
Aliases: wilc.ebam
Keywords: htest
Description: EBAM Analysis Using Wilcoxon Rank Statistics
URL: ../../../library/siggenes/html/wilc.ebam.html

Entry: wilc.stat
Aliases: sam.wilc wilc.stat
Keywords: htest
Description: SAM Analysis Using Wilcoxon Rank Statistics
URL: ../../../library/siggenes/html/wilc.stat.html

Entry: z.ebam
Aliases: z.ebam z.find
Keywords: htest
Description: EBAM analysis Using t- or F-test
URL: ../../../library/siggenes/html/z.ebam.html
