# Easy Microarray data Analysis

## Documentation for package ‘EMA’ version 1.3.1

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## Help Pages

EMA-package | EMA - Easy Microarray Analysis
as.colors | Convert labels to colors
bioMartAnnot | Annotation of probesets using biomaRt
clustering | Agglomerative hierarchical clustering
clustering.kmeans | Kmeans and hierarchical clustering
clustering.plot | Clustering plots for one or two ways representation
distrib.plot | Distribution plots of genes expression level
EMA | EMA - Easy Microarray Analysis
eval.stability.clustering | Compares several clustering methods by means of its stability.
expFilter | Filter expression data
foldchange | Compute foldchange
genes.selection | Genes selection
km | Compute survival curves and test difference between the curves
marty | marty data
marty.type.cl | marty class data for Basal vs HER2 cancer type
multiple.correction | Multiple testing correction
myPalette | Microarray color palette
normAffy | Normalisation of Affymetrix expression arrays
plot3dSample | Sample representation in 3 dimensions for PCA
plotBiplot | Sample and variable representation on a same graph for PCA
plotInertia | Barplot of component inertia percentage for PCA
plotSample | Sample representation for Principal Component Analysis
plotVariable | Variable representation for Principal Component Analysis
PLS | Partial Least Squares
probePlots | Plot the expression profiles of the probes corresponding to given probesets
runGSA | GSA analysis
runHyperGO | Run Gene Ontology analysis based on hypergeometric test from a probeset list
runHyperKEGG | Run KEGG pathway analysis based on hypergeometric test from a probeset list
runIndTest | Computing Differential Analysis for each gene
runMFA | Function to perform a Multiple Factor Analysis.
runPCA | Perform an Principal Component Analysis
runRankprod | Rank product for small samples size
runSAM | SAM analysis with siggenes package
runTtest | Computing Multiple Student Tests
runWilcox | Computing Multiple Wilcoxon Tests
sample.plot | barplot of genes expression level
test.LC | Test linear combinations of parameters of a linear model
test.nested.model | Test for nested ANOVA models