maEndToEnd

DOI: 10.18129/B9.bioc.maEndToEnd    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see maEndToEnd.

An end to end workflow for differential gene expression using Affymetrix microarrays

Bioconductor version: 3.9

In this article, we walk through an end-to-end Affymetrix microarray differential expression workflow using Bioconductor packages. This workflow is directly applicable to current "Gene" type arrays, e.g. the HuGene or MoGene arrays, but can easily be adapted to similar platforms. The data analyzed here is a typical clinical microarray data set that compares inflamed and non-inflamed colon tissue in two disease subtypes. For each disease, the differential gene expression between inflamed- and non-inflamed colon tissue was analyzed. We will start from the raw data CEL files, show how to import them into a Bioconductor ExpressionSet, perform quality control and normalization and finally differential gene expression (DE) analysis, followed by some enrichment analysis.

Author: Bernd Klaus [aut, cre], Stefanie Reisenauer [aut]

Maintainer: Bernd Klaus <bernd.klaus at embl.de>

Installation

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

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

BiocManager::install("maEndToEnd")

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("maEndToEnd")

 

HTML	R Script	An end to end workflow for differential gene expression using Affymetrix microarrays
Text		NEWS

Details

biocViews	GeneExpressionWorkflow, Workflow
Version	2.4.0
License	MIT
Depends	R (>= 3.5.0), Biobase, oligoClasses, ArrayExpress, pd.hugene.1.0.st.v1, hugene10sttranscriptcluster.db, oligo, arrayQualityMetrics, limma, topGO, ReactomePA, clusterProfiler, gplots, ggplot2, geneplotter, pheatmap, RColorBrewer, dplyr, tidyr, stringr, matrixStats, genefilter, openxlsx, Rgraphviz
Imports
LinkingTo
Suggests	BiocStyle, knitr, devtools, rmarkdown
SystemRequirements
Enhances
URL	https://www.bioconductor.org/help/workflows/
Depends On Me
Imports Me
Suggests Me
Links To Me

Package Archives

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

Source Package	maEndToEnd_2.4.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
Source Repository	git clone https://git.bioconductor.org/packages/maEndToEnd
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/maEndToEnd
Package Short Url	https://bioconductor.org/packages/maEndToEnd/
Package Downloads Report	Download Stats