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affy (version 1.50.0)

Methods for Affymetrix Oligonucleotide Arrays

Description

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

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Version

Version

1.50.0

License

LGPL (>= 2.0)

Maintainer

Rafael A Irizarry

Last Published

February 15th, 2017

Functions in affy (1.50.0)

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
make.cl

A Function to Make a Classlabel Vector for Plotting
SpikeIn

SpikeIn Experiment Data: ProbeSet Example
fit.li.wong

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