Easy Microarray data Analysis

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Documentation for package ‘EMA’ version 1.3.2

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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
intersectg Generalized version of intersect for n objects
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
ordinal.chisq Chisq test for ordinal values
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
setdiffg Generalized version of setdiff for n objects
test.LC Test linear combinations of parameters of a linear model
test.nested.model Test for nested ANOVA models