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 |