Package affy
Detailed Description
Title:Methods for Affymetrix Oligonucleotide Arrays Description:The package contains functions for exploratory oligonucleotide array analysis. The dependance to tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.
Author:Rafael A. Irizarry <rafa@jhu.edu>, Laurent Gautier <laurent@cbs.dtu.dk>, Benjamin Milo Bolstad <bolstad@stat.Berkeley.EDU>, and Crispin Miller <cmiller@picr.man.ac.uk> with contributions from Magnus Astrand <Magnus.Astrand@astrazeneca.com>, Leslie M. Cope <cope@mts.jhu.edu>, Robert Gentleman, Jeff Gentry, Conrad Halling <challing@agilixcorp.com>, Wolfgang Huber, James MacDonald <jmacdon@med.umich.edu>, Benjamin I. P. Rubinstein, Christopher Workman <workman@cbs.dtu.dk>, John Zhang Maintainer:Rafael A. Irizarry <rafa@jhu.edu> Version:1.8.1 Built:R 2.2.1; i486-pc-linux-gnu; 2006-03-04 19:51:35; unix Date:2005-09-03 Depends:R (>= 2.0.1), Biobase (>= 1.5.0), methods, utils License:LGPL version 2 or newer Packaged:Sun Oct 16 20:32:47 2005; biocbuild Suggests:tkWidgets (>= 1.2.2), affydata
AffyRNAdeg
Function to assess RNA degradation in Affymetrix GeneChip data.
Last ouput from AffyRNAdeg(). For all plots see PDF file.
PDF output with all plots
Example code and log output is in the "Files" section, please see: affy/AffyRNAdeg/example.log
MAplot
Relative M vs. A plots
Last ouput from MAplot(). For all plots see PDF file.
PDF output with all plots
Example code and log output is in the "Files" section, please see: affy/MAplot/example.log
bg.correct
Background Correction
Last ouput from bg.correct(). For all plots see PDF file.
PDF output with all plots
Example code and log output is in the "Files" section, please see: affy/bg.correct/example.log
fit.li.wong
Fit Li and Wong Model to a Probe Set generate a set of expression values
Last ouput from fit.li.wong(). For all plots see PDF file.
PDF output with all plots
Example code and log output is in the "Files" section, please see: affy/fit.li.wong/example.log
mva.pairs
M vs. A Matrix
Last ouput from mva.pairs(). For all plots see PDF file.
PDF output with all plots
Example code and log output is in the "Files" section, please see: affy/mva.pairs/example.log
plot.ProbeSet
plot a probe set
Last ouput from plot.ProbeSet(). For all plots see PDF file.
PDF output with all plots
Example code and log output is in the "Files" section, please see: affy/plot.ProbeSet/example.log
plotDensity
Plot Densities
Last ouput from plotDensity(). For all plots see PDF file.
PDF output with all plots
Example code and log output is in the "Files" section, please see: affy/plotDensity/example.log
plotLocation
Plot a location on a cel image
Last ouput from plotLocation(). For all plots see PDF file.
PDF output with all plots
Example code and log output is in the "Files" section, please see: affy/plotLocation/example.log
xy2indices
Functions to convert indices to x/y (and reverse)
Last ouput from xy2indices(). For all plots see PDF file.
PDF output with all plots
Example code and log output is in the "Files" section, please see: affy/xy2indices/example.log
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