| calcA |
Method calcA to calculate A values |
| calcA.default |
Method calcA to calculate A values |
| calcA.maigesRaw |
Method calcA to calculate A values |
| calcW |
Method calcW to calculate W values |
| calcW.default |
Method calcW to calculate W values |
| calcW.maigesRaw |
Method calcW to calculate W values |
| classifyKNN |
Function to do discrimination analysis |
| classifyKNNsc |
Function to do discrimination analysis, by the search and choose method |
| classifyLDA |
Function to do discrimination analysis |
| classifyLDAsc |
Function to do discrimination analysis, by the search and choose method |
| classifySVM |
Function to do discrimination analysis |
| classifySVMsc |
Function to do discrimination analysis, by the search and choose method |
| coerce-method |
Coerce a maiges object to classes defined by packages limma and marray |
| 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 only two samples |
| deGenes2by2Ttest |
Function to do differential expression analysis, comparing only two samples |
| deGenes2by2Wilcox |
Function to do differential expression analysis, comparing only two samples |
| deGenesANOVA |
Function to do differential expression analysis, using ANOVA models |
| designANOVA |
Function to construct design an contrasts matrices for ANOVA models |
| dim.maiges |
Retrieve the dimension of microarray objects |
| dim.maigesANOVA |
Retrieve the dimension of microarray objects |
| dim.maigesPreRaw |
Retrieve the dimension of microarray objects |
| dim.maigesRaw |
Retrieve the dimension of microarray objects |
| maiges |
maiges class, store normalised microarray datasets |
| maiges-class |
maiges class, store normalised microarray datasets |
| maigesActMod |
maigesActMod class, store results of functional classification of gene groups |
| maigesActMod-class |
maigesActMod class, store results of functional classification of gene groups |
| maigesActNet |
maigesActNet class, store results of functional classification of gene networks |
| maigesActNet-class |
maigesActNet class, store results of functional classification of gene networks |
| maigesANOVA |
maigesANOVA class, extend maiges class to fit ANOVA models |
| maigesANOVA-class |
maigesANOVA class, extend maiges class to fit ANOVA models |
| maigesClass |
maigesClass class, store results of discrimination (or classification) analysis |
| maigesClass-class |
maigesClass class, store results of discrimination (or classification) analysis |
| maigesDE |
maigesDE class, store results of differential gene expression analysis |
| maigesDE-class |
maigesDE class, store results of differential gene expression analysis |
| maigesDEcluster |
maigesDEcluster class, store results of differential gene expression analysis |
| maigesDEcluster-class |
maigesDEcluster class, store results of differential gene expression analysis |
| maigesPreRaw |
maigesPreRaw class, store pre raw microarray datasets |
| maigesPreRaw-class |
maigesPreRaw class, store pre raw microarray datasets |
| maigesRaw |
maigesRaw class, store raw microarray datasets |
| maigesRaw-class |
maigesRaw class, store raw microarray datasets |
| maigesRelNetB |
maigesRelNetB class, store results of relevance network analysis (Butte's method) |
| maigesRelNetB-class |
maigesRelNetB class, store results of relevance network analysis (Butte's method) |
| maigesRelNetM |
maigesRelNetM class, store results of relevance network analysis (comparing two sample types) |
| maigesRelNetM-class |
maigesRelNetM class, store results of relevance network analysis (comparing two sample types) |
| MI |
Calculate Mutual Information |
| plot |
Method plot for objects defined in this package |
| plot.maiges |
Method plot for objects defined in this package |
| plot.maigesActMod |
Method plot for objects defined in this package |
| plot.maigesActNet |
Method plot for objects defined in this package |
| plot.maigesANOVA |
Method plot for objects defined in this package |
| plot.maigesClass |
Method plot for objects defined in this package |
| plot.maigesDE |
Method plot for objects defined in this package |
| plot.maigesDEcluster |
Method plot for objects defined in this package |
| plot.maigesRaw |
Method plot for objects defined in this package |
| plot.maigesRelNetB |
Method plot for objects defined in this package |
| plot.maigesRelNetM |
Method plot for objects defined in this package |
| plotGenePair |
Scatter plots for pair of genes |
| print |
Method to print a nice visualisation of the objects defined in this package |
| print.maiges |
Method to print a nice visualisation of the objects defined in this package |
| print.maigesActMod |
Method to print a nice visualisation of the objects defined in this package |
| print.maigesActNet |
Method to print a nice visualisation of the objects defined in this package |
| print.maigesANOVA |
Method to print a nice visualisation of the objects defined in this package |
| print.maigesClass |
Method to print a nice visualisation of the objects defined in this package |
| print.maigesDE |
Method to print a nice visualisation of the objects defined in this package |
| print.maigesDEcluster |
Method to print a nice visualisation of the objects defined in this package |
| print.maigesPreRaw |
Method to print a nice visualisation of the objects defined in this package |
| print.maigesRaw |
Method to print a nice visualisation of the objects defined in this package |
| print.maigesRelNetB |
Method to print a nice visualisation of the objects defined in this package |
| print.maigesRelNetM |
Method to print a nice visualisation of the objects defined in this package |