Man pages for EMA
Easy Microarray Data Analysis
| 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 |
