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| a4palette | Utility function that defines a color palette for use in a4 |
| addQuantilesColors | Compute quantiles for plotGeneDE function |
| boxPlot | Create a boxplot for a given gene. |
| combineTwoExpressionSet | Combine two ExpressionSet objects |
| computeLogRatio | Summary statistics for gene expression |
| createExpressionSet | combine gene expression and phenotype data onto a ExpressionSet object |
| ExpressionSetWithComputation-class | Class "ExpressionSetWithComputation" |
| filterVarInt | Filtering on Intensity and Variance |
| heatmap.expressionSet | Image plot of an expressionSet |
| histPvalue | Plot the Distribution of P Values |
| histPvalue-method | Plot the Distribution of P Values |
| histpvalueplotter | Workhorse function for the histPvalue function |
| lassoReg | Multiple regression using the Lasso algorithm as implemented in the glmnet package |
| limmaReg | Wrapper for the limma function for the comparison of two groups (two factor levels) |
| limmaTwoLevels | Wrapper for the limma function for the comparison of two groups (two factor levels) |
| logReg | Logistic regression for predicting the probability to belong to a certain class in binary classification problems |
| nlcvTT | Data to Demonstrate nlcv and Co Functions |
| oaColors | Pick One or More OA Colors |
| oaPalette | Generate a Palette of OA Colors |
| plot1gene | Create a Profile Plot for a given Gene |
| plotComb2Samples | Plots the correlation in gene expression between two samples |
| plotCombination2genes | Plot a Combination of Two Genes |
| plotCombMultSamples | Plots the correlation in gene expression between more than 2 samples |
| plotLogRatio | Plot a summary gene expression graph |
| probabilitiesPlot | Function to plot the probabilities to belong to a certain class in binary classification problems. |
| probe2gene | Translate Affymetrix probeset IDs into gene symbols |
| profilesPlot | Plot expression profiles of multiple genes or probesets Plot expression profiles of multiple genes or probesets. Each line depicts a gene, and the color legend can be used to identify the gene. |
| propDEgenes | Generic function to compute the proportion of differentially expressed genes that are present |
| propDEgenes,limma | Generic function to compute the proportion of differentially expressed genes that are present |
| propDEgenes,numeric | Generic function to compute the proportion of differentially expressed genes that are present |
| propDEgenes-method | Generic function to compute the proportion of differentially expressed genes that are present |
| propDEgenes-methods | Generic function to compute the proportion of differentially expressed genes that are present |
| propdegenescalculation | Estimation of proportion of differentially expressed genes |
| replicates | computes replicates across a vector |
| spectralMap | Generic function to draw a spectral map, according to JnJ Standards |
| spectralMap,ExpressionSet,character | Methods for Function spectralMap according to JnJ Standards |
| spectralMap-method | Methods for Function spectralMap according to JnJ Standards |
| spectralMap-methods | Methods for Function spectralMap according to JnJ Standards |
| topTable,fTest | Methods for topTable |
| topTable,limma | Methods for topTable |
| topTable,MArrayLM | Methods for topTable |
| topTable,tTest | Methods for topTable |
| topTable-method | Methods for topTable |
| topTable-methods | Methods for topTable |
| tTest | Use t Test to Compare Two Groups |
| volcanoPlot | Draw a Volcano Plot |
| volcanoPlot,ExpressionSet,character | Methods for Function spectralMap according to JnJ Standards |
| volcanoPlot,limma,missing,character | Draw a Volcano Plot |
| volcanoPlot,limma,missing,missing | Draw a Volcano Plot |
| volcanoPlot,numeric,numeric,character | Draw a Volcano Plot |
| volcanoPlot,numeric,numeric,missing | Draw a Volcano Plot |
| volcanoPlot,tTest,character | Draw a Volcano Plot |
| volcanoPlot,tTest,missing | Draw a Volcano Plot |
| volcanoPlot-method | Draw a Volcano Plot |
| volcanoPlot-methods | Draw a Volcano Plot |
| volcanoplotter | Workhorse function for the different volcanoPlot methods |