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affy (version 1.44.0)

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

1.44.0

License

LGPL (>= 2.0)

Maintainer

Rafael A Irizarry

Last Published

February 15th, 2017

Functions in affy (1.44.0)

cdfenv.example

Example cdfenv
cdfFromBioC

Functions to obtain CDF files
cleancdfname

Clean Affymetrix's CDF name
maffy.subset

Select Subset
debug.affy123

Debugging Flag
MAplot

Relative M vs. A plots
normalize.qspline

Normalize arrays
normalize.quantiles

Quantile Normalization
affy-deprecated

Deprecated functions in package ‘affy’
affy-options

Options for the affy package
normalize-methods

Normalize Affymetrix Probe Level Data - methods
normalize.contrasts

Normalize intensities using the contrasts method
normalize.invariantset

Invariant Set normalization
normalize.loess

Scale microarray data
probeNames-methods

Methods for accessing the Probe Names
ProbeSet-class

Class ProbeSet
generateExprVal

Compute a summary expression value from the probes intensities
generateExprVal.method.avgdiff

Generate an expression value from the probes informations
justRMA

Read CEL files into an ExpressionSet
list.celfiles

List the Cel Files in a Directory/Folder
ppsetApply

Apply a function over the ProbeSets in an AffyBatch
normalize.quantiles.robust

Robust Quantile Normalization
probeMatch-methods

Methods for accessing perfect matches and mismatches
pairs.AffyBatch

plot intensities using 'pairs'
whatcdf

Find which CDF corresponds
xy2indices

Functions to convert indices to x/y (and reverse)
bg.adjust

Background adjustment (internal function)
bg.correct

Background Correction
hlog

Hybrid Log
generateExprVal.method.playerout

Generate an expression value from the probes informations
mas5calls

MAS 5.0 Absolute Detection
mas5

MAS 5.0 expression measure
plotDensity

Plot Densities
plot.ProbeSet

plot a probe set
barplot.ProbeSet

show a ProbeSet as barplots
AffyRNAdeg

Function to assess RNA degradation in Affymetrix GeneChip data.
expresso

From raw probe intensities to expression values
.setAffyOptions

~~function to set options ~~
summary

Probe Set Summarizing Functions
SpikeIn

SpikeIn Experiment Data: ProbeSet Example
tukey.biweight

One-step Tukey's biweight
plotLocation

Plot a location on a cel image
expressoWidget

A widget for users to pick correction methods
pmcorrect

PM Correction
read.affybatch

Read CEL files into an AffyBatch
ProgressBarText-class

Class "ProgressBarText"
AffyBatch-class

Class AffyBatch
fit.li.wong

Fit Li and Wong Model to a Probe Set
affy.scalevalue.exprSet

Scale normalization for expreSets
generateExprSet-method

generate a set of expression values
merge.AffyBatch

merge two AffyBatch objects
mva.pairs

M vs. A Matrix
read.probematrix

Read CEL file data into PM or MM matrices
rma

Robust Multi-Array Average expression measure