simpleaffy

This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see simpleaffy.

Very simple high level analysis of Affymetrix data


Bioconductor version: 3.9

Provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. Makes heavy use of the affy library. Also has some basic scatter plot functions and mechanisms for generating high resolution journal figures...

Author: Crispin J Miller

Maintainer: Crispin Miller <cmiller at picr.man.ac.uk>

Citation (from within R, enter citation("simpleaffy")):

Installation

To install this package, start R (version "3.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("simpleaffy")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("simpleaffy")
simpleaffy primer PDF R Script
Reference Manual PDF
README Text

Details

biocViews Annotation, DataImport, DifferentialExpression, Microarray, OneChannel, Preprocessing, QualityControl, ReportWriting, Software, Transcription, Visualization
Version 2.60.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 19 years)
License GPL (>= 2)
Depends R (>= 2.0.0), methods, utils, grDevices, graphics, stats, BiocGenerics(>= 0.1.12), Biobase, affy(>= 1.33.6), genefilter, gcrma
Imports methods, utils, grDevices, graphics, stats, BiocGenerics, Biobase, affy, genefilter, gcrma
System Requirements
URL http://www.bioconductor.org http://bioinformatics.picr.man.ac.uk/simpleaffy/
See More
Suggests
Linking To
Enhances
Depends On Me yaqcaffy
Imports Me affyQCReport, arrayMvout
Suggests Me AffyExpress, ArrayTools, ELBOW
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package simpleaffy_2.60.0.tar.gz
Windows Binary simpleaffy_2.60.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) simpleaffy_2.60.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/simpleaffy
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/simpleaffy
Bioc Package Browser https://code.bioconductor.org/browse/simpleaffy/
Package Short Url https://bioconductor.org/packages/simpleaffy/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive