EMA: Easy Microarray Data Analysis

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We propose both a clear analysis strategy and a selection of tools to investigate microarray gene expression data. The most usual and relevant existing R functions were discussed, validated and gathered in an easy-to-use R package (EMA) devoted to gene expression microarray analysis. These functions were improved for ease of use, enhanced visualisation and better interpretation of results.

Author
Nicolas Servant, Eleonore Gravier, Pierre Gestraud, Cecile Laurent, Caroline Paccard, Anne Biton, Jonas Mandel, Bernard Asselain, Emmanuel Barillot, Philippe Hupe
Date of publication
2016-09-07 13:01:55
Maintainer
Pierre Gestraud <pierre.gestraud@curie.fr>
License
GPL-3
Version
1.4.5

View on CRAN

Man pages

as.colors
Convert labels to colors
bioMartAnnot
Annotation of probesets using biomaRt
clust.dist
Computes distances on a data matrix
clustering
Agglomerative hierarchical clustering
clustering.kmeans
Kmeans and hierarchical clustering
clustering.plot
Clustering plots for one or two ways representation
dice
Compute Dice distance on a data matrix
distrib.plot
Distribution plots of genes expression level
EMA-package
EMA - Easy Microarray Analysis
eval.stability.clustering
Compares several clustering methods by means of its...
expFilter
Filter expression data
FDR.BH
FDR.BH
foldchange
Compute foldchange
FWER.Bonf
Multiple testing correction using FWER
genes.selection
Genes selection
goReport
Text report from the 'hyperGTest' function
GSA.correlate.txt
Correlation between Genes collection and Genes Array
htmlheader
htmlheader
htmlresult
Html report from the result of the 'hyperGTest' function
intersectg
Generalized version of intersect for n objects
inverse
inverse
jaccard
Compute Jaccard distance on a data matrix
keggReport
Text report from the result of the 'hyperGTest' function for...
km
Compute survival curves and test difference between the...
makeAllContrasts
Create all pairwise contrasts
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...
multiple.correction
Multiple testing correction
myPalette
Microarray color palette
normAffy
Normalisation of Affymetrix expression arrays
ordinal.chisq
Chisq test for ordinal values
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...
qualitySample
Sample quality computation in PCA
runGSA
GSA analysis
runHyperGO
Run Gene Ontology analysis based on hypergeometric test from...
runHyperKEGG
Run KEGG pathway analysis based on hypergeometric test from a...
runIndTest
Computing Differential Analysis for each gene
runMFA
Function to perform a Multiple Factor Analysis.
runPCA
Perform an Principal Component Analysis
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

Files in this package

EMA
EMA/NAMESPACE
EMA/NEWS
EMA/data
EMA/data/marty.RData
EMA/data/datalist
EMA/R
EMA/R/EMA-internal.R
EMA/R/utils.R
EMA/R/pca.R
EMA/R/explore.R
EMA/R/anadiff.R
EMA/R/clustering.R
EMA/R/survival.R
EMA/R/norm.R
EMA/R/zzz.R
EMA/R/anafunc.R
EMA/MD5
EMA/DESCRIPTION
EMA/man
EMA/man/multiple.correction.Rd
EMA/man/EMA-package.Rd
EMA/man/runHyperGO.Rd
EMA/man/clustering.kmeans.Rd
EMA/man/clust.dist.Rd
EMA/man/marty.type.cl.Rd
EMA/man/PLS.Rd
EMA/man/keggReport.Rd
EMA/man/probePlots.Rd
EMA/man/distrib.plot.Rd
EMA/man/dice.Rd
EMA/man/test.LC.Rd
EMA/man/setdiffg.Rd
EMA/man/MFAreport.Rd
EMA/man/sample.plot.Rd
EMA/man/inverse.Rd
EMA/man/km.Rd
EMA/man/runMFA.Rd
EMA/man/FDR.BH.Rd
EMA/man/runGSA.Rd
EMA/man/expFilter.Rd
EMA/man/runIndTest.Rd
EMA/man/makeAllContrasts.Rd
EMA/man/ordinal.chisq.Rd
EMA/man/htmlheader.Rd
EMA/man/bioMartAnnot.Rd
EMA/man/clustering.Rd
EMA/man/normAffy.Rd
EMA/man/runSAM.Rd
EMA/man/plotVariable.Rd
EMA/man/GSA.correlate.txt.Rd
EMA/man/plotInertia.Rd
EMA/man/intersectg.Rd
EMA/man/plotBiplot.Rd
EMA/man/runHyperKEGG.Rd
EMA/man/goReport.Rd
EMA/man/qualitySample.Rd
EMA/man/genes.selection.Rd
EMA/man/as.colors.Rd
EMA/man/htmlresult.Rd
EMA/man/marty.Rd
EMA/man/jaccard.Rd
EMA/man/plotSample.Rd
EMA/man/clustering.plot.Rd
EMA/man/test.nested.model.Rd
EMA/man/runPCA.Rd
EMA/man/myPalette.Rd
EMA/man/foldchange.Rd
EMA/man/runWilcox.Rd
EMA/man/eval.stability.clustering.Rd
EMA/man/runTtest.Rd
EMA/man/FWER.Bonf.Rd