Workflow Package: maEndToEnd

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

Bioconductor version: Release (3.8)

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>

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

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("maEndToEnd", version = "3.8")

Documentation

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

browseVignettes("maEndToEnd")

 

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Details

biocViews GeneExpressionWorkflow, Workflow
Version 2.0.0
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
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Enhances
URL https://www.bioconductor.org/help/workflows/
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