affy v1.50.0

Methods for Affymetrix Oligonucleotide Arrays

The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.

Functions in affy

Name Description
ProbeSet-class Class ProbeSet
generateExprVal.method.avgdiff Generate an expression value from the probes informations
cdfenv.example Example cdfenv
normalize.quantiles.robust Robust Quantile Normalization
list.celfiles List the Cel Files in a Directory/Folder
mva.pairs M vs. A Matrix
plotILM plotILM
affycompPlot Assessment Plots
probeNames-methods Methods for accessing the Probe Names
assessSD SD Assessment functions
remove.hgu133a.xhyb Remove crosshybridizers
AffyRNAdeg Function to assess RNA degradation in Affymetrix GeneChip data.
affy-deprecated Deprecated functions in package ‘affy’
assessAll Assessment functions
summary Probe Set Summarizing Functions
internal functions Internal affyPLM functions
mas5.assessment Example of the result of assessments
affycomp.figures.auxiliary Auxiliary functions to create Figures
generateExprVal.method.pdnn Compute PM correction and summary expression value
ilm affyILM
pca.legend A Function to Automagically Place a Legend in a PCA Plot
titlePage QC report title page with array names
exprset.log Take log base 2 of Expression
normalize.constant Scale probe intensities
normalize.invariantset Invariant Set normalization
normalize.qspline Normalize arrays
assessSpikeIn2 New Assessment functions for Spike In Data
rma Robust Multi-Array Average expression measure
rmaPara Parallelized PMA preprocessing
affycoretools Make repetitive analyses of microarray and RNA-Seq data simpler with affycoretools.
generateExprVal Compute a summary expression value from the probes intensities
makeIndices Create Indices for Venn Diagrams
gsHeatmap A function to create a simple heatmap and key.
cdfFromBioC Functions to obtain CDF files
normalizeAffyBatchLoessIterPara Parallelized partial loess normalization with permutation
vsnPara Parallel fir of the vsn model
justRMA Read CEL files into an ExpressionSet
normalizeAffyBatchConstantPara Parallelized scaling normalization
maplot Relative M vs. A plots
SD SD Assessment Functions
matplotProbesPDNN Plot the PDNN computed probe intensities
ILM-class Class to contain the results of an ilm calculation
pseudo.coloring Coloring pseudo chip images
MAplotPara Parallelized relative M vs. A plots for Microarray Data
ReadRMAExpress Read RMAExpress computed expression values
venn4Way 4-way Venn Diagrams
expressopdnn Position Dependant Nearest Neighbors model for affy
computeExprSetPara Parallel generate a set of expression values
affycomp.compfigs.auxiliary Auxiliary functions to create comparitive Figures A Function to Make a Classlabel Vector for Plotting
SpikeIn SpikeIn Experiment Data: ProbeSet Example Fit Li and Wong Model to a Probe Set
expresso From raw probe intensities to expression values
normalize.loess Scale microarray data
plotLocation Plot a location on a cel image
mergeSplitObjects Merge a list of split objects
read.affybatch Read CEL files into an AffyBatch
distributeFiles Distribute files to slaves
readAffybatchPara Parallelized Read-AffyBatch function
plotIntens plotIntens
removeDistributedFiles Remove distributed files from slaves
normalize.ExpressionSet Normalization applied to ExpressionSets
affystart Pre-processing for Affymetrix Data
threestepPLM Three Step expression measures returned as a PLMset
QCReport QC Report for AffyBatch objects
getMainProbes Remove control probesets from ST arrays
plotDeg Functions to Plot Density and RNA Degradation Plots
ALGchangeLog affylmGUI Change Log
geneSetPage A function to create an HTML page for each gene set, as well as the HTML pages for each significant gene set.
pdnn.params.chiptype A function to fit PDNN parameters
makeHmap A function to create a heatmap-like object or matrix of correlations between miRNA and mRNA data.
runRomer A function to run the romer function on a set of contrasts.
get.celfile.dates Extract Dates from CEL files
hgu133a.pdnn.params Chip-type specific data
find.params.pdnn A function to find the experiment specific PDNN parameters
read.celfile.header Read header information from cel file
transform.ProbeSet A function to transform a ProbeSet
cleancdfname Clean Affymetrix's CDF name
plotDensity Plot Densities
pmcorrect PM Correction
ppsetApply Apply a function over the ProbeSets in an AffyBatch
normalize.quantiles Quantile Normalization
xy2indices Functions to convert indices to x/y (and reverse)
AffyBatch-class Class AffyBatch
bg.correct.LESN LESN - Low End Signal is Noise Background corrections
affy-options Options for the affy package
hgu133a.spikein.phenodata phenotypic information for HGU133A spike in study
check.cdf.type CDF file format function
assessSpikeIn Assessment functions for Spike In Data
bg.adjust Background adjustment (internal function)
hlog Hybrid Log
ProgressBarText-class Class "ProgressBarText"
normalize.contrasts Normalize intensities using the contrasts method
tukey.biweight One-step Tukey's biweight
threestep Three Step expression measures
affy.scalevalue.exprSet Scale normalization for expreSets
normalize-methods Normalize Affymetrix Probe Level Data - methods
splitObjects Functions to split objects into parts
PLMset2exprSet Convert a PLMset to an ExpressionSet
borderQC2 Center of intensity QC plots
boxplotPara Parallelized Box Plots for Microarray Data
makeGoTable Create HTML tables for Gene Ontology (GO) analyses
annotateEset Method to annotate ExpressionSets automatically
assessDilution Assessment functions for Dilution Data
normalizeAffyBatchLoessPara Parallelized loess normalization
normalize.quantiles.probeset Quantile Normalization applied to probesets
mirna2mrna A function to map miRNA to mRNA.
getCols Correct Ordering of Contrasts
rmaPLM Fit a RMA to Affymetrix Genechip Data as a PLMset
vennCounts2 Compute Counts for Venn Diagram
vennSelect2 Select and Output Genelists Based on Venn Diagrams
affylmGUI Graphical User Interface for the limma microarray package
barplot.ProbeSet show a ProbeSet as barplots
generateExprVal.method.playerout Generate an expression value from the probes informations
maffy.subset Select Subset
plot.ProbeSet plot a probe set
setRectRegion set a rectangular or circular region in an affybatch to a specified set of values
preprocess Background correct and Normalize
normalize.scaling Scaling normalization
read.probematrix Read CEL file data into PM or MM matrices
generateExprSet-method generate a set of expression values
mas5 MAS 5.0 expression measure
qa Parallel Quality Assessment Summary
ilm-methods Methods to access the results of ilm.
probeMatch-methods Methods for accessing perfect matches and mismatches
.setAffyOptions ~~function to set options ~~
preproPara Parallelized preprocessing
affycompTable Expression Assessment Table
signalDist Intensity distribution plots for a AffyBatch object
bgCorrectPara Parallelized Background Correction
expressoWidget A widget for users to pick correction methods
vsnInputPara Class to contain input data and parameters for parallel vsn functions
snow-startstop Starting and Stopping SNOW Clusters
normalizeAffyBatchInvariantsetPara Parallelized Invariante Set normalization
vennPage High-level function for making Venn diagrams with clickable links to HTML pages with the underlying genes.
affyQAReport Generate a QA Report for Affymetrix arrays
params.dilution Parameters for the Dilution dataset
makeGoGeneTable Make Gene table from GO analysis results
tableFilt Filter a topTable object
normalizeAffyBatchQuantilesPara Parallelized quantile normalization
correlationPlot Array-array intensity correlation plot
spikein.phenodata phenotypic information for spike in study
intNames Create Names for Venn Diagram Intersections
hgu133a.spikein.xhyb Cross hybridizers
makeVenn High-level function for making Venn diagrams and outputting the results from the diagrams in HTML and CSV files.
writeFit Function to output annotated fit data from limma
read.celfile.probeintensity.matrices Read PM or MM from CEL file into matrices
bg.correct Background Correction
debug.affy123 Debugging Flag
pairs.AffyBatch plot intensities using 'pairs'
merge.AffyBatch merge two AffyBatch objects
whatcdf Find which CDF corresponds
fitPLM Fit a Probe Level Model to Affymetrix Genechip Data.
PLMset-class Class PLMset
mas5calls MAS 5.0 Absolute Detection
dilution.phenodata Phenotypic Information for Dilution Study
borderQC1 Distribution of intensities of the border elements
dataAndHeatmapPage A function to create an annotated HTML table for all genes in a significant gene set as well as a heatmap of these data.
entrezLinks Add links to data when using ReportingTools
readin Read Expression Date Sets
makeImages Add dotplot images
fixHeaderAndGo Fix data.frame header for use with ReportingTools
affycoretools-defunct Defunct functions in package affycoretools
plotPCA A Function to Make a PCA Plot from an ExpressionSet
read.celfile Read a CEL file into an R list
outputRomer A function to create HTML output from the results of running romer on a set of contrasts.
read.cdffile.list Read CDF file into an R list
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LinkingTo preprocessCore
License LGPL (>= 2.0)
Collate ProgressBarText.R ppset.ttest.R ppsetApply.R expressoWidget.R getCDFenv.R AffyRNAdeg.R avdiff.R barplot.ProbeSet.R bg.Affy.chipwide.R bg.R expresso.R generateExprVal.method.avgdiff.R generateExprVal.method.liwong.R generateExprVal.method.mas.R generateExprVal.method.medianpolish.R generateExprVal.method.playerout.R hlog.R justrma.R loess.normalize.R maffy.R mas5.R merge.AffyBatch.R normalize.constant.R normalize.contrasts.R normalize.invariantset.R normalize.loess.R normalize.qspline.R normalize.quantiles.R pairs.AffyBatch.R plot.density.R plotLocation.R plot.ProbeSet.R pmcorrect.mas.R AffyBatch.R mva.pairs.R ProbeSet.R read.affybatch.R rma.R summary.R tukey.biweight.R whatcdf.R xy2indices.R zzz.R
biocViews Microarray, OneChannel, Preprocessing
LazyLoad yes

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