Entry: Fstat
Aliases: Fstat
Keywords: models
Description: Calculation of F statistic by gene given a linear model
URL: ../../../library/SAGx/html/Fstat.html

Entry: GSEA.mean.t
Aliases: GSEA.mean.t
Keywords: multivariate
Description: Gene Set Enrichment Analysis using output from samroc
URL: ../../../library/SAGx/html/GSEA.mean.t.html

Entry: JT.test
Aliases: JT.test
Keywords: nonparametric
Description: Jonckheere-Terpstra trend test
URL: ../../../library/SAGx/html/JT.test.html

Entry: R2BASE
Aliases: R2BASE
Keywords: models
Description: Produces a BASE file
URL: ../../../library/SAGx/html/R2BASE.html

Entry: R2mim
Aliases: R2mim
Keywords: multivariate
Description: Output a script file to WinMIM
URL: ../../../library/SAGx/html/R2mim.html

Entry: Xprep
Aliases: Xprep
Keywords: models
Description: Fitting of a linear model
URL: ../../../library/SAGx/html/Xprep.html

Entry: Xprep.resid
Aliases: Xprep.resid
Keywords: models
Description: Calculation of input of residuals from linear model
URL: ../../../library/SAGx/html/Xprep.resid.html

Entry: clin2mim
Aliases: clin2mim
Keywords: multivariate
Description: Output a script file to WinMIM, linking clinical data and gene expression
URL: ../../../library/SAGx/html/clin2mim.html

Entry: cluster.q
Aliases: cluster.q
Keywords: multivariate
Description: Clustering Goodness measured by Q2
URL: ../../../library/SAGx/html/cluster.q.html

Entry: estimatep0
Aliases: estimatep0
Keywords: htest
Description: Estimate proportion unchanged genes
URL: ../../../library/SAGx/html/estimatep0.html

Entry: fetchSignal
Aliases: fetchSignal
Keywords: database
Description: Fetch data from the GATC database
URL: ../../../library/SAGx/html/fetchSignal.html

Entry: firstpass
Aliases: firstpass
Keywords: nonparametric
Description: First pass description of GeneChip data
URL: ../../../library/SAGx/html/firstpass.html

Entry: fom
Aliases: fom
Keywords: multivariate
Description: Clustering Figure of Merit
URL: ../../../library/SAGx/html/fom.html

Entry: fp.fn
Aliases: fp.fn
Keywords: htest
Description: Calculation of fp and fn based on a vector of p-values
URL: ../../../library/SAGx/html/fp.fn.html

Entry: gap
Aliases: gap
Keywords: multivariate
Description: GAP statistic clustering figure of merit
URL: ../../../library/SAGx/html/gap.html

Entry: list.experiments
Aliases: list.experiments
Keywords: database
Description: Display all experiment names and id's
URL: ../../../library/SAGx/html/list.experiments.html

Entry: list.intersection.p
Aliases: list.intersection.p
Keywords: distribution
Description: p-value for intersection of two gene lists.
URL: ../../../library/SAGx/html/list.intersection.p.html

Entry: mat2TeX
Aliases: mat2TeX
Keywords: IO
Description: Ouput matrix to LaTeX
URL: ../../../library/SAGx/html/mat2TeX.html

Entry: myclus
Aliases: myclus
Keywords: multivariate
Description: A clustering function
URL: ../../../library/SAGx/html/myclus.html

Entry: normalise
Aliases: normalise
Keywords: multivariate
Description: Normalise arrays
URL: ../../../library/SAGx/html/normalise.html

Entry: one.probeset.per.gene
Aliases: one.probeset.per.gene
Keywords: multivariate
Description: Select the best probeset per gene
URL: ../../../library/SAGx/html/one.probeset.per.gene.html

Entry: outlier
Aliases: outlier
Keywords: multivariate
Description: Identify outliers in the multivariate distribution
URL: ../../../library/SAGx/html/outlier.html

Entry: p0.mom
Aliases: p0.mom
Keywords: nonparametric
Description: Estimate proportion unchanged genes
URL: ../../../library/SAGx/html/p0.mom.html

Entry: pava.fdr
Aliases: pava.fdr
Keywords: htest
Description: Estimate of the FDR and the proportion unchanged genes
URL: ../../../library/SAGx/html/pava.fdr.html

Entry: pava
Aliases: pava
Keywords: regression
Description: Pooling of Adjacent Violators
URL: ../../../library/SAGx/html/pava.html

Entry: rank.genes
Aliases: rank.genes
Keywords: multivariate
Description: Rank genes with respect to multiple criteria
URL: ../../../library/SAGx/html/rank.genes.html

Entry: rank.trend
Aliases: rank.trend
Keywords: robust
Description: Trens analysis based on ranks
URL: ../../../library/SAGx/html/rank.trend.html

Entry: rsd.test
Aliases: rsd.test
Keywords: nonparametric
Description: Compare two groups with respect to their RSD (CV)
URL: ../../../library/SAGx/html/rsd.test.html

Entry: samroc.result-class
Aliases: samroc.result-class show,samroc.result-method plot,samroc.result-method
Keywords: methods
Description: Class "samroc.result" for results of the function samrocN
URL: ../../../library/SAGx/html/samroc.result-class.html

Entry: samrocN
Aliases: samrocN
Keywords: htest
Description: Calculate ROC curve based SAM statistic
URL: ../../../library/SAGx/html/samrocn.html

Entry: samrocNboot
Aliases: samrocNboot
Keywords: htest
Description: Calculate ROC curve based SAM statistic
URL: ../../../library/SAGx/html/samrocnboot.html

Entry: union.of.pways
Aliases: union.of.pways
Keywords: multivariate
Description: Create the union of two pathway lists
URL: ../../../library/SAGx/html/union.of.pways.html
