| activeMod | Functional classification of gene groups |
| activeModScoreHTML | Save HTML file with global gene scores from functional gene... |
| activeNet | Functional classification of gene networks |
| activeNetScoreHTML | Save HTML file with scores and p-values from functional gene... |
| addGeneGrps | Function to load gene groups into maigesPreRaw object |
| addPaths | Function to load gene pathways into maigesPreRaw object |
| bootstrapCor | Calculate bootstrap p-values for correlation measures |
| bootstrapMI | Calculate bootstrap p-values for mutual information (MI)... |
| bootstrapT | Calculate bootstrap p-values for t statistics |
| boxplot-methods | Method boxplot for objects defined in this package |
| bracketMethods | Sub-setting methods for maiges objects |
| calcA | Method calcA to calculate A values |
| calcW | Method calcW to calculate W values |
| classifyKNN | Function to do discrimination analysis |
| classifyKNNsc | Function to do discrimination analysis, by the search and... |
| classifyLDA | Function to do discrimination analysis |
| classifyLDAsc | Function to do discrimination analysis, by the search and... |
| classifySVM | Function to do discrimination analysis |
| classifySVMsc | Function to do discrimination analysis, by the search and... |
| coerce-methods | Coerce a maiges object to classes defined by packages limma... |
| compCorr | Compute correlation differences and their p-values |
| contrastsFitM | Compute Contrasts from Linear Model Fit |
| createMaigesRaw | Function to create objects of class maigesRaw |
| createTDMS | Create a tab delimited file for TIGR MeV |
| deGenes2by2BootT | Function to do differential expression analysis, comparing... |
| deGenes2by2Ttest | Function to do differential expression analysis, comparing... |
| deGenes2by2Wilcox | Function to do differential expression analysis, comparing... |
| deGenesANOVA | Function to do differential expression analysis, using ANOVA... |
| designANOVA | Function to construct design an contrasts matrices for ANOVA... |
| dim-methods | Retrieve the dimension of microarray objects |
| gastro | Gastro-esophagic dataset |
| getLabels | Method getLabels to pick gene and sample labels |
| heatmapsM | Function to plot heatmaps separating groups generated by SOM... |
| hierM | Function to do hierarchical cluster analysis |
| hierMde | Function to do hierarchical cluster analysis |
| image-methods | Method image for objects defined in this package |
| kmeansM | Function to do k-means cluster analysis |
| kmeansMde | Function to do k-means cluster analysis |
| loadData | Load cDNA microarray data tables |
| maigesActMod-class | maigesActMod class, store results of functional... |
| maigesActNet-class | maigesActNet class, store results of functional... |
| maigesANOVA-class | maigesANOVA class, extend maiges class to fit ANOVA models |
| maiges-class | maiges class, store normalised microarray datasets |
| maigesClass-class | maigesClass class, store results of discrimination (or... |
| maigesDE-class | maigesDE class, store results of differential gene expression... |
| maigesDEcluster-class | maigesDEcluster class, store results of differential gene... |
| maigesPreRaw-class | maigesPreRaw class, store pre raw microarray datasets |
| maigesRaw-class | maigesRaw class, store raw microarray datasets |
| maigesRelNetB-class | maigesRelNetB class, store results of relevance network... |
| maigesRelNetM-class | maigesRelNetM class, store results of relevance network... |
| MI | Calculate Mutual Information |
| normLoc | Normalise a cDNA Microarray Object |
| normOLIN | Normalise a cDNA Microarray Object |
| normRepLoess | Bootstrap of LOWESS normalisation |
| normScaleLimma | Scale adjust a cDNA Microarray Object |
| normScaleMarray | Scale adjust a cDNA Microarray Object |
| plotGenePair | Scatter plots for pair of genes |
| plot-methods | Method plot for objects defined in this package |
| print-methods | Method to print a nice visualisation of the objects defined... |
| relNet2TGF | Transform Relevance Network analysis in TGF output |
| relNetworkB | Relevance Network analysis |
| relNetworkM | Relevance Network analysis |
| robustCorr | Calculate a robust correlation value |
| selSpots | Select spots to use in normalisation |
| show-methods | Show a nice visualisation of the objects defined in this... |
| somM | Function to do SOM cluster analysis |
| somMde | Function to do SOM cluster analysis |
| summarizeReplicates | Summarise microarray objects |
| summary-methods | Method summary for the object from this package |
| tableClass | Save HTML or CSV tables of good classifiers (cliques) |
| tablesDE | Save HTML or CSV tables of differentially expressed genes |
