Package sma
Detailed Description
Title:Statistical Microarray Analysis Description:The package contains some simple functions for exploratory microarray analysis.
Author:Sandrine Dudoit <sandrine@stat.berkeley.edu> Yee Hwa (Jean) Yang <yeehwa@stat.berkeley.edu> Benjamin Milo Bolstad <bolstad@stat.Berkeley.EDU>, with contributions from Natalie Thorne <thorne@wehi.edu.au> Ingrid L?nnstedt <ingrid@math.uu.se> Jessica Mar Maintainer:Benjamin M. Bolstad <bmb@bmbolstad.com> Version:0.5.15 Built:R 2.2.1; ; 2006-02-11 19:01:52; unix Date:2005/11/15 Depends:R (>= 1.3.0) License:GPL version 2 or newer Packaged:Tue Nov 15 14:32:17 2005; bmb URL:http://www.stat.berkeley.edu/users/terry/zarray/Html/smacode.html
plot.bayesian
Plots lodscore vs effect estimate (the output of stat.bayesian() or stat.bay.est()).
Last ouput from plot.bayesian(). For all plots see PDF file.
PDF output with all plots
Example code and log output is in the "Files" section, please see: sma/plot.bayesian/example.log
plot.confband.lines
Adding Lines Satisfying a Confidence Criterion to the Current M vs A Plot
Last ouput from plot.confband.lines(). For all plots see PDF file.
PDF output with all plots
Example code and log output is in the "Files" section, please see: sma/plot.confband.lines/example.log
plot.confband.points
Highlights a Set of Points on the Current M vs A Plot
Last ouput from plot.confband.points(). For all plots see PDF file.
PDF output with all plots
Example code and log output is in the "Files" section, please see: sma/plot.confband.points/example.log
plot.confband.text
Add Selected Text to an M vs A Plot
Last ouput from plot.confband.text(). For all plots see PDF file.
PDF output with all plots
Example code and log output is in the "Files" section, please see: sma/plot.confband.text/example.log
plot.mat
Red and Green Color Image of Data Matrix
Last ouput from plot.mat(). For all plots see PDF file.
PDF output with all plots
Example code and log output is in the "Files" section, please see: sma/plot.mat/example.log
plot.mva
M vs. A Plot
Last ouput from plot.mva(). For all plots see PDF file.
PDF output with all plots
Example code and log output is in the "Files" section, please see: sma/plot.mva/example.log
plot.scale.box
Box plots for microarray
Last ouput from plot.scale.box(). For all plots see PDF file.
PDF output with all plots
Example code and log output is in the "Files" section, please see: sma/plot.scale.box/example.log
plot.smooth.line
Adding Lowess Lines to Current Plot
Last ouput from plot.smooth.line(). For all plots see PDF file.
PDF output with all plots
Example code and log output is in the "Files" section, please see: sma/plot.smooth.line/example.log
plot.spatial
Spatial Representation of Microarray Spot Statistics
Last ouput from plot.spatial(). For all plots see PDF file.
PDF output with all plots
Example code and log output is in the "Files" section, please see: sma/plot.spatial/example.log
plot.svb
Plot of Signal vs. Background
Last ouput from plot.svb(). For all plots see PDF file.
PDF output with all plots
Example code and log output is in the "Files" section, please see: sma/plot.svb/example.log
stat.Chen
Apply Chen's single slide method
Last ouput from stat.Chen(). For all plots see PDF file.
PDF output with all plots
Example code and log output is in the "Files" section, please see: sma/stat.Chen/example.log
stat.ChurSap
Apply Sapir and Churchills single slide method
Last ouput from stat.ChurSap(). For all plots see PDF file.
PDF output with all plots
Example code and log output is in the "Files" section, please see: sma/stat.ChurSap/example.log
stat.Newton
Apply Newtons single slide method
Last ouput from stat.Newton(). For all plots see PDF file.
PDF output with all plots
Example code and log output is in the "Files" section, please see: sma/stat.Newton/example.log
stat.bay.est
Calculates an Odds Ratio for Each Gene in a Multi-slide Microarray Experiment.
Last ouput from stat.bay.est(). For all plots see PDF file.
PDF output with all plots
Example code and log output is in the "Files" section, please see: sma/stat.bay.est/example.log
stat.bayesian
Calculates an Odds Ratio of Each Gene in a Multi-slide microarray Experiment
Last ouput from stat.bayesian(). For all plots see PDF file.
PDF output with all plots
Example code and log output is in the "Files" section, please see: sma/stat.bayesian/example.log
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