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a4Base (version 1.16.0)
Automated Affymetrix Array Analysis Base Package
Description
Automated Affymetrix Array Analysis
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Version
1.20.0
1.18.0
1.16.0
1.14.0
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Version
1.16.0
License
GPL-3
Maintainer
Tobias Verbeke
Last Published
October 2nd, 2013
Functions in a4Base (1.16.0)
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boxPlot
Create a boxplot for a given gene.
histpvalueplotter
Workhorse function for the histPvalue function
combineTwoExpressionSet
Combine two ExpressionSet objects
lassoReg
Multiple regression using the Lasso algorithm as implemented in the glmnet package
propDEgenes
Generic function to compute the proportion of differentially expressed genes that are present
propdegenescalculation
Estimation of proportion of differentially expressed genes
tTest
Use t Test to Compare Two Groups
volcanoPlot-methods
Draw a Volcano Plot
propDEgenes-methods
Methods for propDEgenes
profilesPlot
Plot expression profiles of multiple genes or probesets
a4palette
Utility function that defines a color palette for use in a4
addQuantilesColors
Compute quantiles for plotGeneDE function
plotLogRatio
Plot a summary gene expression graph
plotCombMultSamples
Plots the correlation in gene expression between more than 2 samples
probabilitiesPlot
Function to plot the probabilities to belong to a certain class in binary classification problems.
probe2gene
Translate Affymetrix probeset IDs into gene symbols
ExpressionSetWithComputation-class
Class "ExpressionSetWithComputation"
limmaTwoLevels
Wrapper function for the comparison of two groups using limma
filterVarInt
Filter Features On Intensity and Variance
logReg
Logistic regression for predicting the probability to belong to a certain class in binary classification problems.
replicates
computes replicates across a vector
spectralMap-methods
Methods for Function spectralMap
computeLogRatio
Summary statistics for gene expression
createExpressionSet
combine gene expression and phenotype data onto a ExpressionSet object
plotComb2Samples
Plots the correlation in gene expression between two samples
plotCombination2genes
Plot a Combination of Two Genes
volcanoPlot
Draw a Volcano Plot
volcanoplotter
Workhorse function for the different volcanoPlot methods
heatmap.expressionSet
Image plot of an expressionSet
histPvalue
Plot the Distribution of P Values
nlcvTT
Data to Demonstrate nlcv and Co Functions
plot1gene
Create a Profile Plot for a given Gene
spectralMap
Draw a Spectral Map
topTable-methods
Methods for topTable