Partial Least Squares
Normalisation of Affymetrix expression arrays
Microarray color palette
Convert labels to colors
Compute Jaccard distance on a data matrix
Create all pairwise contrasts
Genes selection
Computing Multiple Student Tests
Annotation of probesets using biomaRt
Html report from the result of the 'hyperGTest' function
Multiple testing correction using FWER
Plot the expression profiles of the probes corresponding to given probesets
Function to perform a Multiple Factor Analysis.
Filter expression data
Run Gene Ontology analysis based on hypergeometric test from a probeset list
Variable representation for Principal Component Analysis
Computes distances on a data matrix
Sample quality computation in PCA
Computing Differential Analysis for each gene
Run KEGG pathway analysis based on hypergeometric test from a probeset list
Perform an Principal Component Analysis
Multiple testing correction
EMA - Easy Microarray Analysis
Generalized version of setdiff for n objects
Barplot of component inertia percentage for PCA
FDR.BH
Kmeans and hierarchical clustering
Correlation between Genes collection and Genes Array
Compute foldchange
barplot of genes expression level
Generalized version of intersect for n objects
Compute survival curves and test difference between the curves
Chisq test for ordinal values
marty data
Sample representation for Principal Component Analysis
SAM analysis with siggenes package
GSA analysis
Clustering plots for one or two ways representation
marty class data for Basal vs HER2 cancer type
Test linear combinations of parameters of a linear model
Compute Dice distance on a data matrix
Test for nested ANOVA models
htmlheader
Text report from the result of the 'hyperGTest' function for KEGG
pathway analysis
Distribution plots of genes expression level
Sample and variable representation on a same graph for PCA
Agglomerative hierarchical clustering
Computing Multiple Wilcoxon Tests
eval.stability.clustering
Compares several clustering methods by means of its stability.
Text report from the 'hyperGTest' function
inverse
Function to create a txt and pdf report with the main statistics
and graphics of the MFA.