Functional genomic technologies like microarrays, sequencing, and mass spectrometry enable scientists to gather unbiased measurements of gene expression levels on a genome-wide scale. Whether you are generating your own data or want to explore the large number of publicly available data sets, you will first need to learn how to analyze these types of experiments. In this course, you will be taught how to use the versatile R/Bioconductor package limma to perform a differential expression analysis on the most common experimental designs. Furthermore, you will learn how to pre-process the data, identify and correct for batch effects, visually assess the results, and perform enrichment testing. After completing this course, you will have general analysis strategies for gaining insight from any functional genomics study.
To begin, you'll review the goals of differential expression analysis, manage gene expression data using R and Bioconductor, and run your first differential expression analysis with limma.
In this chapter, you'll learn how to construct linear models to test for differential expression for common experimental designs.
Now that you've learned how to perform differential expression tests, next you'll learn how to normalize and filter the feature data, check for technical batch effects, and assess the results.
In this final chapter, you'll use your new skills to perform an end-to-end differential expression analysis of a study that uses a factorial design to assess the impact of the cancer drug doxorubicin on the hearts of mice with different genetic backgrounds.
In the following tracksAnalyzing Genomic Data
PrerequisitesIntroduction to Statistics in R
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