a4Base: Automated Affymetrix Array Analysis Base Package

Automated Affymetrix Array Analysis

AuthorWillem Talloen, Tobias Verbeke, Tine Casneuf, An De Bondt, Steven Osselaer and Hinrich Goehlmann, Willem Ligtenberg
Date of publicationNone
MaintainerTobias Verbeke <tobias.verbeke@openanalytics.eu>, Willem Ligtenberg <willem.ligtenberg@openanalytics.eu>
LicenseGPL-3
Version1.22.0

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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