activeMod |
Functional classification of gene groups |
activeModScoreHTML |
Save HTML file with global gene scores from functional gene groups classification |
activeNet |
Functional classification of gene networks |
activeNetScoreHTML |
Save HTML file with scores and p-values from functional gene networks classification |
addGeneGrps |
Function to load gene groups into maigesPreRaw object |
addPaths |
Function to load gene pathways into maigesPreRaw object |
as |
Coerce a maiges object to classes defined by packages limma and marray |
as,maiges,MAList-method |
Coerce a maiges object to classes defined by packages limma and marray |
as,maiges,marrayNorm-method |
Coerce a maiges object to classes defined by packages limma and marray |
as,maigesRaw,marrayRaw-method |
Coerce a maiges object to classes defined by packages limma and marray |
as,maigesRaw,RGList-method |
Coerce a maiges object to classes defined by packages limma and marray |
as,MAList,maiges-method |
Coerce a maiges object to classes defined by packages limma and marray |
as,marrayNorm,maiges-method |
Coerce a maiges object to classes defined by packages limma and marray |
as,marrayRaw,maigesRaw-method |
Coerce a maiges object to classes defined by packages limma and marray |
as,RGList,maigesRaw-method |
Coerce a maiges object to classes defined by packages limma and marray |
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 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,maiges,MAList-method |
Coerce a maiges object to classes defined by packages limma and marray |
coerce,maiges,marrayNorm-method |
Coerce a maiges object to classes defined by packages limma and marray |
coerce,maigesRaw,marrayRaw-method |
Coerce a maiges object to classes defined by packages limma and marray |
coerce,maigesRaw,RGList-method |
Coerce a maiges object to classes defined by packages limma and marray |
coerce,MAList,maiges-method |
Coerce a maiges object to classes defined by packages limma and marray |
coerce,marrayNorm,maiges-method |
Coerce a maiges object to classes defined by packages limma and marray |
coerce,marrayRaw,maigesRaw-method |
Coerce a maiges object to classes defined by packages limma and marray |
coerce,RGList,maigesRaw-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 |
selSpots |
Select spots to use in normalisation |
show |
Show a nice visualisation of the objects defined in this package |
show,maiges-method |
Show a nice visualisation of the objects defined in this package |
show,maigesActMod-method |
Show a nice visualisation of the objects defined in this package |
show,maigesActNet-method |
Show a nice visualisation of the objects defined in this package |
show,maigesANOVA-method |
Show a nice visualisation of the objects defined in this package |
show,maigesClass-method |
Show a nice visualisation of the objects defined in this package |
show,maigesDE-method |
Show a nice visualisation of the objects defined in this package |
show,maigesDEcluster-method |
Show a nice visualisation of the objects defined in this package |
show,maigesPreRaw-method |
Show a nice visualisation of the objects defined in this package |
show,maigesRaw-method |
Show a nice visualisation of the objects defined in this package |
show,maigesRelNetB-method |
Show a nice visualisation of the objects defined in this package |
show,maigesRelNetM-method |
Show a nice visualisation of the objects defined in this package |
somM |
Function to do SOM cluster analysis |
somMde |
Function to do SOM cluster analysis |
summarizeReplicates |
Summarise microarray objects |
summary |
Method summary for the object from this package |