Easy Microarray data Analysis


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Documentation for package ‘EMA’ version 1.1

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ABCIS-package What the package does (short line) ~~ package title ~~
EMA-package EMA - Easy Microarray Analysis
ABCIS What the package does (short line) ~~ package title ~~
as.colors Data to Colors
bioMartAnnot Annotation using bioMart
clust.dist Computes distances on a data matrix
clustering agglomerative hierarchical clustering.
clustering.kmeans Kmeans and hierarchical clustering
clustering.plot clustering plot
dice Compute Dice distance on a data matrix
distrib.plot distribution plot of genes expression level
EMA EMA - Easy Microarray Analysis
eval.stability.clustering Compares several clustering methods by means of its stability.
expFilter A function to filter expression data.
foldchange foldchange
FWER.Bonf FWER.Bonf
genes.selection genes selection
goReport Text report from the result of a call to 'hyperGTest' for GO category
GSA.correlate.txt Correlation between Genes collection and Genes Array
htmlresult Html report from the result of a call to 'hyperGTest'
jaccard Compute Jaccard distance on a data matrix
keggReport Text report from the result of a call to 'hyperGTest' for KEGG pathway
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
MFAreport Function to create a txt and pdf report with the main statistics and graphics of the MFA.
mult.clustering multiple clustering
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
plotExplore Distribution analysis of each column (arrays) of a gene expression matrix
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
qualitySample Sample quality computation in PCA
runGSA GSA analysis with !!! GSA package (Corrected by P.N.) !!!
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