Entry: MI
Aliases: MI
Keywords: methods
Description: Calculate Mutual Information
URL: ../../../library/maigesPack/html/MI.html

Entry: activeMod
Aliases: activeMod
Keywords: methods
Description: Functional classification of gene groups
URL: ../../../library/maigesPack/html/activeMod.html

Entry: activeModScoreHTML
Aliases: activeModScoreHTML
Keywords: methods
Description: Save HTML file with global gene scores from functional gene groups classification
URL: ../../../library/maigesPack/html/activeModScoreHTML.html

Entry: activeNet
Aliases: activeNet
Keywords: methods
Description: Functional classification of gene networks
URL: ../../../library/maigesPack/html/activeNet.html

Entry: activeNetScoreHTML
Aliases: activeNetScoreHTML
Keywords: methods
Description: Save HTML file with scores and p-values from functional gene networks classification
URL: ../../../library/maigesPack/html/activeNetScoreHTML.html

Entry: addGeneGrps
Aliases: addGeneGrps
Keywords: methods
Description: Function to load gene groups into maigesPreRaw object
URL: ../../../library/maigesPack/html/addGeneGrps.html

Entry: addPaths
Aliases: addPaths
Keywords: methods
Description: Function to load gene pathways into maigesPreRaw object
URL: ../../../library/maigesPack/html/addPaths.html

Entry: bootstrapCor
Aliases: bootstrapCor
Keywords: methods
Description: Calculate bootstrap p-values for correlation measures
URL: ../../../library/maigesPack/html/bootstrapCor.html

Entry: bootstrapMI
Aliases: bootstrapMI
Keywords: methods
Description: Calculate bootstrap p-values for mutual information (MI) measures
URL: ../../../library/maigesPack/html/bootstrapMI.html

Entry: bootstrapT
Aliases: bootstrapT
Keywords: methods
Description: Calculate bootstrap p-values for t statistics
URL: ../../../library/maigesPack/html/bootstrapT.html

Entry: boxplot
Aliases: boxplot.maigesRaw boxplot.maiges boxplot.maigesANOVA boxplot.maigesDEcluster boxplot
Keywords: array
Description: Method boxplot for objects defined in this package
URL: ../../../library/maigesPack/html/boxplot-methods.html

Entry: [-method
Aliases: [,maiges-method [,maigesANOVA-method [,maigesRaw-method [,maigesPreRaw-method [
Keywords: methods
Description: Sub-setting methods for maiges objects
URL: ../../../library/maigesPack/html/bracketMethods.html

Entry: calcA
Aliases: calcA.default calcA.maigesRaw calcA
Keywords: array
Description: Method calcA to calculate A values
URL: ../../../library/maigesPack/html/calcA.html

Entry: calcW
Aliases: calcW.default calcW.maigesRaw calcW
Keywords: array
Description: Method calcW to calculate W values
URL: ../../../library/maigesPack/html/calcW.html

Entry: classifyKNN
Aliases: classifyKNN
Keywords: methods
Description: Function to do discrimination analysis
URL: ../../../library/maigesPack/html/classifyKNN.html

Entry: classifyKNNsc
Aliases: classifyKNNsc
Keywords: methods
Description: Function to do discrimination analysis, by the search and choose method
URL: ../../../library/maigesPack/html/classifyKNNsc.html

Entry: classifyLDA
Aliases: classifyLDA
Keywords: methods
Description: Function to do discrimination analysis
URL: ../../../library/maigesPack/html/classifyLDA.html

Entry: classifyLDAsc
Aliases: classifyLDAsc
Keywords: methods
Description: Function to do discrimination analysis, by the search and choose method
URL: ../../../library/maigesPack/html/classifyLDAsc.html

Entry: classifySVM
Aliases: classifySVM
Keywords: methods
Description: Function to do discrimination analysis
URL: ../../../library/maigesPack/html/classifySVM.html

Entry: classifySVMsc
Aliases: classifySVMsc
Keywords: methods
Description: Function to do discrimination analysis, by the search and choose method
URL: ../../../library/maigesPack/html/classifySVMsc.html

Entry: coerce-method
Aliases: coerce,maiges,marrayNorm-method coerce,marrayNorm,maiges-method coerce,maiges,MAList-method coerce,MAList,maiges-method coerce,maigesRaw,marrayRaw-method coerce,marrayRaw,maigesRaw-method coerce,maigesRaw,RGList-method coerce,RGList,maigesRaw-method as,maiges,marrayNorm-method as,marrayNorm,maiges-method as,maiges,MAList-method as,MAList,maiges-method as,maigesRaw,marrayRaw-method as,marrayRaw,maigesRaw-method as,maigesRaw,RGList-method as,RGList,maigesRaw-method as
Keywords: methods
Description: Coerce a maiges object to classes defined by packages limma and marray
URL: ../../../library/maigesPack/html/coerce-methods.html

Entry: compCorr
Aliases: compCorr
Keywords: methods
Description: Compute correlation differences and their p-values
URL: ../../../library/maigesPack/html/compCorr.html

Entry: contrastsFitM
Aliases: contrastsFitM
Keywords: methods
Description: Compute Contrasts from Linear Model Fit
URL: ../../../library/maigesPack/html/contrastsFitM.html

Entry: createMaigesRaw
Aliases: createMaigesRaw
Keywords: methods
Description: Function to create objects of class maigesRaw
URL: ../../../library/maigesPack/html/createMaigesRaw.html

Entry: createTDMS
Aliases: createTDMS
Keywords: methods
Description: Create a tab delimited file for TIGR MeV
URL: ../../../library/maigesPack/html/createTDMS.html

Entry: deGenes2by2BootT
Aliases: deGenes2by2BootT
Keywords: methods
Description: Function to do differential expression analysis, comparing only two samples
URL: ../../../library/maigesPack/html/deGenes2by2BootT.html

Entry: deGenes2by2Ttest
Aliases: deGenes2by2Ttest
Keywords: methods
Description: Function to do differential expression analysis, comparing only two samples
URL: ../../../library/maigesPack/html/deGenes2by2Ttest.html

Entry: deGenes2by2Wilcox
Aliases: deGenes2by2Wilcox
Keywords: methods
Description: Function to do differential expression analysis, comparing only two samples
URL: ../../../library/maigesPack/html/deGenes2by2Wilcox.html

Entry: deGenesANOVA
Aliases: deGenesANOVA
Keywords: methods
Description: Function to do differential expression analysis, using ANOVA models
URL: ../../../library/maigesPack/html/deGenesANOVA.html

Entry: designANOVA
Aliases: designANOVA
Keywords: methods
Description: Function to construct design an contrasts matrices for ANOVA models
URL: ../../../library/maigesPack/html/designANOVA.html

Entry: dim
Aliases: dim.maiges dim.maigesRaw dim.maigesPreRaw dim.maigesANOVA
Keywords: array
Description: Retrieve the dimension of microarray objects
URL: ../../../library/maigesPack/html/dim-methods.html

Entry: gastro
Aliases: gastro gastro.raw gastro.raw2 gastro.norm gastro.summ
Keywords: datasets
Description: Gastro-esophagic dataset
URL: ../../../library/maigesPack/html/gastro.html

Entry: getLabels
Aliases: getLabels.default getLabels.maigesDE getLabels.maigesDEcluster getLabels.RGList getLabels.MAList getLabels.marrayRaw getLabels.marrayNorm getLabels
Keywords: array
Description: Method getLabels to pick gene and sample labels
URL: ../../../library/maigesPack/html/getLabels.html

Entry: heatmapsM
Aliases: heatmapsM
Keywords: hplot
Description: Function to plot heatmaps separating groups generated by SOM or k-means
URL: ../../../library/maigesPack/html/heatmapsM.html

Entry: hierM
Aliases: hierM
Keywords: hplot
Description: Function to do hierarchical cluster analysis
URL: ../../../library/maigesPack/html/hierM.html

Entry: hierMde
Aliases: hierMde
Keywords: hplot
Description: Function to do hierarchical cluster analysis
URL: ../../../library/maigesPack/html/hierMde.html

Entry: image
Aliases: image.maigesRaw image.maiges image.maigesANOVA image.maigesRelNetB image.maigesRelNetM image.maigesActMod image.maigesActNet image
Keywords: array
Description: Method image for objects defined in this package
URL: ../../../library/maigesPack/html/image-methods.html

Entry: kmeansM
Aliases: kmeansM
Keywords: hplot
Description: Function to do k-means cluster analysis
URL: ../../../library/maigesPack/html/kmeansM.html

Entry: kmeansMde
Aliases: kmeansMde
Keywords: hplot
Description: Function to do k-means cluster analysis
URL: ../../../library/maigesPack/html/kmeansMde.html

Entry: loadData
Aliases: loadData
Keywords: file
Description: Load cDNA microarray data tables
URL: ../../../library/maigesPack/html/loadData.html

Entry: maiges-class
Aliases: maiges-class maiges
Keywords: classes
Description: maiges class, store normalised microarray datasets
URL: ../../../library/maigesPack/html/maiges-class.html

Entry: maigesANOVA-class
Aliases: maigesANOVA-class maigesANOVA
Keywords: classes
Description: maigesANOVA class, extend maiges class to fit ANOVA models
URL: ../../../library/maigesPack/html/maigesANOVA-class.html

Entry: maigesActMod-class
Aliases: maigesActMod-class maigesActMod
Keywords: classes
Description: maigesActMod class, store results of functional classification of gene groups
URL: ../../../library/maigesPack/html/maigesActMod-class.html

Entry: maigesActNet-class
Aliases: maigesActNet-class maigesActNet
Keywords: classes
Description: maigesActNet class, store results of functional classification of gene networks
URL: ../../../library/maigesPack/html/maigesActNet-class.html

Entry: maigesClass-class
Aliases: maigesClass-class maigesClass
Keywords: classes
Description: maigesClass class, store results of discrimination (or classification) analysis
URL: ../../../library/maigesPack/html/maigesClass-class.html

Entry: maigesDE-class
Aliases: maigesDE-class maigesDE
Keywords: classes
Description: maigesDE class, store results of differential gene expression analysis
URL: ../../../library/maigesPack/html/maigesDE-class.html

Entry: maigesDEcluster-class
Aliases: maigesDEcluster-class maigesDEcluster
Keywords: classes
Description: maigesDEcluster class, store results of differential gene expression analysis
URL: ../../../library/maigesPack/html/maigesDEcluster-class.html

Entry: maigesPreRaw-class
Aliases: maigesPreRaw-class maigesPreRaw
Keywords: classes
Description: maigesPreRaw class, store pre raw microarray datasets
URL: ../../../library/maigesPack/html/maigesPreRaw-class.html

Entry: maigesRaw-class
Aliases: maigesRaw-class maigesRaw
Keywords: classes
Description: maigesRaw class, store raw microarray datasets
URL: ../../../library/maigesPack/html/maigesRaw-class.html

Entry: maigesRelNetB-class
Aliases: maigesRelNetB-class maigesRelNetB
Keywords: classes
Description: maigesRelNetB class, store results of relevance network analysis (Butte's method)
URL: ../../../library/maigesPack/html/maigesRelNetB-class.html

Entry: maigesRelNetM-class
Aliases: maigesRelNetM-class maigesRelNetM
Keywords: classes
Description: maigesRelNetM class, store results of relevance network analysis (comparing two sample types)
URL: ../../../library/maigesPack/html/maigesRelNetM-class.html

Entry: normLoc
Aliases: normLoc
Keywords: classes
Description: Normalise a cDNA Microarray Object
URL: ../../../library/maigesPack/html/normLoc.html

Entry: normOLIN
Aliases: normOLIN
Keywords: classes
Description: Normalise a cDNA Microarray Object
URL: ../../../library/maigesPack/html/normOLIN.html

Entry: normRepLoess
Aliases: normRepLoess
Keywords: methods
Description: Bootstrap of LOWESS normalisation
URL: ../../../library/maigesPack/html/normRepLoess.html

Entry: normScaleLimma
Aliases: normScaleLimma
Keywords: classes
Description: Scale adjust a cDNA Microarray Object
URL: ../../../library/maigesPack/html/normScaleLimma.html

Entry: normScaleMarray
Aliases: normScaleMarray
Keywords: classes
Description: Scale adjust a cDNA Microarray Object
URL: ../../../library/maigesPack/html/normScaleMarray.html

Entry: plot
Aliases: plot.maigesRaw plot.maiges plot.maigesANOVA plot.maigesDE plot.maigesDEcluster plot.maigesClass plot.maigesRelNetB plot.maigesRelNetM plot.maigesActMod plot.maigesActNet plot
Keywords: array
Description: Method plot for objects defined in this package
URL: ../../../library/maigesPack/html/plot-methods.html

Entry: plotGenePair
Aliases: plotGenePair
Keywords: classes
Description: Scatter plots for pair of genes
URL: ../../../library/maigesPack/html/plotGenePair.html

Entry: print
Aliases: print.maigesPreRaw print.maigesRaw print.maiges print.maigesANOVA print.maigesDE print.maigesDEcluster print.maigesClass print.maigesRelNetB print.maigesRelNetM print.maigesActMod print.maigesActNet print
Keywords: array
Description: Method to print a nice visualisation of the objects defined in this package
URL: ../../../library/maigesPack/html/print-methods.html

Entry: relNet2TGF
Aliases: relNet2TGF.maigesRelNetB relNet2TGF.maigesRelNetM relNet2TGF
Keywords: classes
Description: Transform Relevance Network analysis in TGF output
URL: ../../../library/maigesPack/html/relNet2TGF.html

Entry: relNetworkB
Aliases: relNetworkB
Keywords: methods
Description: Relevance Network analysis
URL: ../../../library/maigesPack/html/relNetworkB.html

Entry: relNetworkM
Aliases: relNetworkM
Keywords: methods
Description: Relevance Network analysis
URL: ../../../library/maigesPack/html/relNetworkM.html

Entry: robustCorr
Aliases: robustCorr
Keywords: methods
Description: Calculate a robust correlation value
URL: ../../../library/maigesPack/html/robustCorr.html

Entry: selSpots
Aliases: selSpots
Keywords: classes
Description: Select spots to use in normalisation
URL: ../../../library/maigesPack/html/selSpots.html

Entry: show-method
Aliases: show,maigesPreRaw-method show,maigesRaw-method show,maiges-method show,maigesANOVA-method show,maigesDE-method show,maigesDEcluster-method show,maigesClass-method show,maigesRelNetB-method show,maigesRelNetM-method show,maigesActMod-method show,maigesActNet-method show
Keywords: methods
Description: Show a nice visualisation of the objects defined in this package
URL: ../../../library/maigesPack/html/show-methods.html

Entry: somM
Aliases: somM
Keywords: hplot
Description: Function to do SOM cluster analysis
URL: ../../../library/maigesPack/html/somM.html

Entry: somMde
Aliases: somMde
Keywords: hplot
Description: Function to do SOM cluster analysis
URL: ../../../library/maigesPack/html/somMde.html

Entry: summarizeReplicates
Aliases: summarizeReplicates
Keywords: classes
Description: Summarise microarray objects
URL: ../../../library/maigesPack/html/summarizeReplicates.html

Entry: summary
Aliases: summary.maigesPreRaw summary.maigesRaw summary.maiges summary.maigesANOVA summary.maigesDE summary.maigesDEcluster summary.maigesClass summary.maigesRelNetB summary.maigesRelNetM summary.maigesActMod summary.maigesActNet summary
Keywords: array
Description: Method summary for the object from this package
URL: ../../../library/maigesPack/html/summary-methods.html

Entry: tableClass
Aliases: tableClass
Keywords: methods
Description: Save HTML or CSV tables of good classifiers (cliques)
URL: ../../../library/maigesPack/html/tableClass.html

Entry: tablesDE
Aliases: tablesDE
Keywords: methods
Description: Save HTML or CSV tables of differentially expressed genes
URL: ../../../library/maigesPack/html/tablesDE.html
