simpleaffy

DOI: 10.18129/B9.bioc.simpleaffy    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.12 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: 3.12

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 "4.0") and enter:

if (!requireNamespace("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")

 

PDF R Script simpleaffy primer
PDF   Reference Manual
Text   README

Details

biocViews Annotation, DataImport, DifferentialExpression, Microarray, OneChannel, Preprocessing, QualityControl, ReportWriting, Software, Transcription, Visualization
Version 2.66.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier (> 16 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
LinkingTo
Suggests
SystemRequirements
Enhances
URL http://www.bioconductor.org http://bioinformatics.picr.man.ac.uk/simpleaffy/
Depends On Me yaqcaffy
Imports Me affyQCReport, arrayMvout
Suggests Me AffyExpress, ArrayTools, ELBOW
Links To Me
Build Report  

Package Archives

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

Source Package simpleaffy_2.66.0.tar.gz
Windows Binary simpleaffy_2.66.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) simpleaffy_2.66.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/simpleaffy
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/simpleaffy
Package Short Url https://bioconductor.org/packages/simpleaffy/
Package Downloads Report Download Stats

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