affy

Class AffyBatch

Function to assess RNA degradation in Affymetrix GeneChip data.

Relative M vs. A plots

Class ProbeSet

Class "ProgressBarText"

SpikeIn Experiment Data: ProbeSet Example

Deprecated functions in package ‘affy’

Options for the affy package

Scale normalization for expreSets

show a ProbeSet as barplots

Background adjustment (internal function)

Background Correction

Functions to obtain CDF files

Example cdfenv

Clean Affymetrix's CDF name

Debugging Flag

From raw probe intensities to expression values

A widget for users to pick correction methods

Fit Li and Wong Model to a Probe Set

generate a set of expression values

Compute a summary expression value from the probes intensities

Generate an expression value from the probes informations

Generate an expression value from the probes informations

Hybrid Log

Read CEL files into an ExpressionSet

List the Cel Files in a Directory/Folder

Select Subset

MAS 5.0 expression measure

MAS 5.0 Absolute Detection

merge two AffyBatch objects

M vs. A Matrix

Normalize Affymetrix Probe Level Data - methods

Scale probe intensities

Normalize intensities using the contrasts method

Invariant Set normalization

Scale microarray data

Normalize arrays

Quantile Normalization

Robust Quantile Normalization

plot intensities using 'pairs'

plot a probe set

Plot Densities

Plot a location on a cel image

PM Correction

Apply a function over the ProbeSets in an AffyBatch

Methods for accessing perfect matches and mismatches

Methods for accessing the Probe Names

Read CEL files into an AffyBatch

Read CEL file data into PM or MM matrices

Robust Multi-Array Average expression measure

~~function to set options ~~

Probe Set Summarizing Functions

One-step Tukey's biweight

Find which CDF corresponds

Functions to convert indices to x/y (and reverse)