a4Base: Automated Affymetrix Array Analysis Base Package

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Automated Affymetrix Array Analysis

Author
Willem Talloen, Tobias Verbeke, Tine Casneuf, An De Bondt, Steven Osselaer and Hinrich Goehlmann, Willem Ligtenberg
Date of publication
None
Maintainer
Tobias Verbeke <tobias.verbeke@openanalytics.eu>, Willem Ligtenberg <willem.ligtenberg@openanalytics.eu>
License
GPL-3
Version
1.22.0

View on Bioconductor

Man pages

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...
ExpressionSetWithComputation
Class "ExpressionSetWithComputation"
filterVarInt
Filter Features On Intensity and Variance
heatmap.expressionSet
Image plot of an expressionSet
histPvalue
Plot the Distribution of P Values
histpvalueplotter
Workhorse function for the histPvalue function
lassoReg
Multiple regression using the Lasso algorithm as implemented...
limmaTwoLevels
Wrapper function for the comparison of two groups using limma
logReg
Logistic regression for predicting the probability to belong...
nlcvTT
Data to Demonstrate nlcv and Co Functions
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...
plotLogRatio
Plot a summary gene expression graph
probabilitiesPlot
Function to plot the probabilities to belong to a certain...
probe2gene
Translate Affymetrix probeset IDs into gene symbols
profilesPlot
Plot expression profiles of multiple genes or probesets
propDEgenes
Generic function to compute the proportion of differentially...
propdegenescalculation
Estimation of proportion of differentially expressed genes
propDEgenes-methods
Methods for propDEgenes
replicates
computes replicates across a vector
spectralMap
Draw a Spectral Map
spectralMap-methods
Methods for Function spectralMap
topTable-methods
Methods for topTable
tTest
Use t Test to Compare Two Groups
volcanoPlot
Draw a Volcano Plot
volcanoPlot-methods
Draw a Volcano Plot
volcanoplotter
Workhorse function for the different volcanoPlot methods

Files in this package

a4Base/DESCRIPTION
a4Base/NAMESPACE
a4Base/R
a4Base/R/addQuantilesColors.R
a4Base/R/allClasses.R
a4Base/R/computeLogRatio.R
a4Base/R/exprSetManipulations.R
a4Base/R/filtering.R
a4Base/R/heatmap.R
a4Base/R/histPvalue.R
a4Base/R/lassoReg.R
a4Base/R/limma.R
a4Base/R/logisticRegression.R
a4Base/R/plotLogRatio.R
a4Base/R/plotSmoothScat.R
a4Base/R/probe2gene.R
a4Base/R/profilePlot.R
a4Base/R/propDEgenes.R
a4Base/R/replicates.R
a4Base/R/spectralMap.R
a4Base/R/tTest.R
a4Base/R/volcanoPlot.R
a4Base/R/zzz.R
a4Base/data
a4Base/data/nlcvTT.rda
a4Base/inst
a4Base/inst/NEWS
a4Base/inst/TODO
a4Base/inst/etc
a4Base/inst/etc/tooltip.script
a4Base/man
a4Base/man/ExpressionSetWithComputation.Rd
a4Base/man/a4palette.Rd
a4Base/man/addQuantilesColors.Rd
a4Base/man/boxPlot.Rd
a4Base/man/combineTwoExpressionSet.Rd
a4Base/man/computeLogRatio.Rd
a4Base/man/createExpressionSet.Rd
a4Base/man/filterVarInt.Rd
a4Base/man/heatmap.expressionSet.Rd
a4Base/man/histPvalue.Rd
a4Base/man/histpvalueplotter.Rd
a4Base/man/lassoReg.Rd
a4Base/man/limmaTwoLevels.Rd
a4Base/man/logReg.Rd
a4Base/man/nlcvTT.Rd
a4Base/man/plot1gene.Rd
a4Base/man/plotComb2Samples.Rd
a4Base/man/plotCombMultSamples.Rd
a4Base/man/plotCombination2genes.Rd
a4Base/man/plotLogRatio.Rd
a4Base/man/probabilitiesPlot.Rd
a4Base/man/probe2gene.Rd
a4Base/man/profilesPlot.Rd
a4Base/man/propDEgenes-methods.Rd
a4Base/man/propDEgenes.Rd
a4Base/man/propdegenescalculation.Rd
a4Base/man/replicates.Rd
a4Base/man/spectralMap-methods.Rd
a4Base/man/spectralMap.Rd
a4Base/man/tTest.Rd
a4Base/man/topTable-methods.Rd
a4Base/man/volcanoPlot-methods.Rd
a4Base/man/volcanoPlot.Rd
a4Base/man/volcanoplotter.Rd