An end to end workflow for differential gene expression using Affymetrix microarrays
Introduction | Workflow package installation from Bioconductor | Workflow package import | List of packages required for the workflow | Downloading the raw data from ArrayExpress | Background information on the data | Information stored in ArrayExpress | Bioconductor ExpressionSets | Import of annotation data and microarray expression data as "ExpressionSet" | Quality control of the raw data | Background adjustment, calibration, summarization and annotation | Background adjustment | Across-array normalization (calibration) | Summarization | Old and new "probesets" of Affymetrix microarrays | One-step preprocessing in oligo | Relative Log Expression data quality analysis | Computing the RLE | Plotting the RLE | RMA calibration of the data | Some mathematical background on normalization (calibration) and background correction | Quality assessment of the calibrated data | Filtering based on intensity | Annotation of the transcript clusters | Removing multiple mappings | Building custom annotations | Linear models | Linear models for microarrays | A linear model for the data | Analysis of differential expression based on a single gene | Contrasts and hypotheses tests | Extracting results | Multiple testing FDR, and comparison with results from the original paper | Visualization of DE analysis results - volcano plot | Gene ontology (GO) based enrichment analysis | Matching the background set of genes | Running topGO | Visualization of the GO-analysis results | A pathway enrichment analysis using reactome | Visualizing the reactome based analysis results | Session information | Acknowledgements | Author Contributions | References
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