Man pages for Bioconductor-mirror/maigesPack
Functions to handle cDNA microarray data, including several methods of data analysis

activeModFunctional classification of gene groups
activeModScoreHTMLSave HTML file with global gene scores from functional gene...
activeNetFunctional classification of gene networks
activeNetScoreHTMLSave HTML file with scores and p-values from functional gene...
addGeneGrpsFunction to load gene groups into maigesPreRaw object
addPathsFunction to load gene pathways into maigesPreRaw object
bootstrapCorCalculate bootstrap p-values for correlation measures
bootstrapMICalculate bootstrap p-values for mutual information (MI)...
bootstrapTCalculate bootstrap p-values for t statistics
boxplot-methodsMethod boxplot for objects defined in this package
bracketMethodsSub-setting methods for maiges objects
calcAMethod calcA to calculate A values
calcWMethod calcW to calculate W values
classifyKNNFunction to do discrimination analysis
classifyKNNscFunction to do discrimination analysis, by the search and...
classifyLDAFunction to do discrimination analysis
classifyLDAscFunction to do discrimination analysis, by the search and...
classifySVMFunction to do discrimination analysis
classifySVMscFunction to do discrimination analysis, by the search and...
coerce-methodsCoerce a maiges object to classes defined by packages limma...
compCorrCompute correlation differences and their p-values
contrastsFitMCompute Contrasts from Linear Model Fit
createMaigesRawFunction to create objects of class maigesRaw
createTDMSCreate a tab delimited file for TIGR MeV
deGenes2by2BootTFunction to do differential expression analysis, comparing...
deGenes2by2TtestFunction to do differential expression analysis, comparing...
deGenes2by2WilcoxFunction to do differential expression analysis, comparing...
deGenesANOVAFunction to do differential expression analysis, using ANOVA...
designANOVAFunction to construct design an contrasts matrices for ANOVA...
dim-methodsRetrieve the dimension of microarray objects
gastroGastro-esophagic dataset
getLabelsMethod getLabels to pick gene and sample labels
heatmapsMFunction to plot heatmaps separating groups generated by SOM...
hierMFunction to do hierarchical cluster analysis
hierMdeFunction to do hierarchical cluster analysis
image-methodsMethod image for objects defined in this package
kmeansMFunction to do k-means cluster analysis
kmeansMdeFunction to do k-means cluster analysis
loadDataLoad cDNA microarray data tables
maigesActMod-classmaigesActMod class, store results of functional...
maigesActNet-classmaigesActNet class, store results of functional...
maigesANOVA-classmaigesANOVA class, extend maiges class to fit ANOVA models
maiges-classmaiges class, store normalised microarray datasets
maigesClass-classmaigesClass class, store results of discrimination (or...
maigesDE-classmaigesDE class, store results of differential gene expression...
maigesDEcluster-classmaigesDEcluster class, store results of differential gene...
maigesPreRaw-classmaigesPreRaw class, store pre raw microarray datasets
maigesRaw-classmaigesRaw class, store raw microarray datasets
maigesRelNetB-classmaigesRelNetB class, store results of relevance network...
maigesRelNetM-classmaigesRelNetM class, store results of relevance network...
MICalculate Mutual Information
normLocNormalise a cDNA Microarray Object
normOLINNormalise a cDNA Microarray Object
normRepLoessBootstrap of LOWESS normalisation
normScaleLimmaScale adjust a cDNA Microarray Object
normScaleMarrayScale adjust a cDNA Microarray Object
plotGenePairScatter plots for pair of genes
plot-methodsMethod plot for objects defined in this package
print-methodsMethod to print a nice visualisation of the objects defined...
relNet2TGFTransform Relevance Network analysis in TGF output
relNetworkBRelevance Network analysis
relNetworkMRelevance Network analysis
robustCorrCalculate a robust correlation value
selSpotsSelect spots to use in normalisation
show-methodsShow a nice visualisation of the objects defined in this...
somMFunction to do SOM cluster analysis
somMdeFunction to do SOM cluster analysis
summarizeReplicatesSummarise microarray objects
summary-methodsMethod summary for the object from this package
tableClassSave HTML or CSV tables of good classifiers (cliques)
tablesDESave HTML or CSV tables of differentially expressed genes
Bioconductor-mirror/maigesPack documentation built on June 1, 2017, 11:44 a.m.