a4Base: Automated Affymetrix Array Analysis Base Package

Automated Affymetrix Array Analysis

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("a4Base")
AuthorWillem Talloen, Tobias Verbeke, Tine Casneuf, An De Bondt, Steven Osselaer and Hinrich Goehlmann, Willem Ligtenberg
Bioconductor views Microarray
Date of publicationNone
MaintainerTobias Verbeke <tobias.verbeke@openanalytics.eu>, Willem Ligtenberg <willem.ligtenberg@openanalytics.eu>
LicenseGPL-3
Version1.24.0

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

Functions

a4palette Man page
addQuantilesColors Man page
boxPlot Man page
combineTwoExpressionSet Man page
computeLogRatio Man page
createExpressionSet Man page
ExpressionSetWithComputation-class Man page
filterVarInt Man page
heatmap.expressionSet Man page
histPvalue Man page
histPvalue,limma-method Man page
histPvalue,MArrayLM-method Man page
histPvalue,numeric-method Man page
histpvalueplotter Man page
histPvalue,tTest-method Man page
lassoReg Man page
limmaTwoLevels Man page
logReg Man page
nlcvTT Man page
plot1gene Man page
plotComb2Samples Man page
plotCombination2genes Man page
plotCombMultSamples Man page
plotLogRatio Man page
probabilitiesPlot Man page
probe2gene Man page
profilesPlot Man page
propDEgenes Man page
propdegenescalculation Man page
propDEgenes,limma-method Man page
propDEgenes-methods Man page
propDEgenes,numeric-method Man page
replicates Man page
spectralMap Man page
spectralMap,ExpressionSet,character-method Man page
spectralMap-methods Man page
topTable,fTest-method Man page
topTable,glmnet-method Man page
topTable,limma-method Man page
topTable,MArrayLM-method Man page
topTable-methods Man page
topTable,pamClass-method Man page
topTable,rfClass-method Man page
topTable,tTest-method Man page
tTest Man page
volcanoPlot Man page
volcanoPlot,limma,missing,character-method Man page
volcanoPlot,limma,missing,missing-method Man page
volcanoPlot-methods Man page
volcanoPlot,numeric,numeric,character-method Man page
volcanoPlot,numeric,numeric,missing-method Man page
volcanoplotter Man page
volcanoPlot,tTest,missing,character-method Man page
volcanoPlot,tTest,missing,missing-method Man page

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

Please suggest features or report bugs with the GitHub issue tracker.

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