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

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

Entry: ebam.wilc
Aliases: ebam.wilc
Keywords: htest
Description: Empirical Bayes Analysis using Wilcoxon Rank Sums
URL: ../../../library/siggenes/html/ebam.wilc.html

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

Entry: fudge2
Aliases: fudge2
Keywords: optimize
Description: Fudge Factor
URL: ../../../library/siggenes/html/fudge2.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 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: na.handling
Aliases: na.handling
Keywords: utilities
Description: Handling of Missing Values
URL: ../../../library/siggenes/html/na.handling.html

Entry: na.replace.cont
Aliases: na.replace.cont
Keywords: utilities
Description: Replacing of Missing Values in Continuous Data
URL: ../../../library/siggenes/html/na.replace.cont.html

Entry: na.replace.dist
Aliases: na.replace.dist
Keywords: utilities
Description: Handling of Missing Values in Categorical Data
URL: ../../../library/siggenes/html/na.replace.dist.html

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

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

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

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

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

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

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

Entry: sam2excel
Aliases: sam2excel
Keywords: IO file
Description: CSV file of a SAM object
URL: ../../../library/siggenes/html/sam2excel.html

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

Entry: siggenes-internal
Aliases: adjust.for.mt build.dperm cat.stat d.null d.stat pairt.cl.transform pairt.samp pairt.samp.transform Rfold.cal setup.mat.samp stats.cal wilc.stat ebam.old ebam.wilc.old find.a0.old neglogLik.repeat q.value.old q.value.wilc R.fold.old ratio.est rs.cal sam.sampler xy.cal p0.est quantiles add.target2href check.chipname col2hex getTD4Affy make.tablecode pretty.mat.fdr formatSAM pretty.mat.sig
Keywords: internal
Description: Internal siggenes functions
URL: ../../../library/siggenes/html/siggenes-internal.html

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