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 |