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Bioinformatics with R Cookbook by Paurush Praveen Sinha

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Analyzing RNAseq data with the edgeR package

In order to determine whether the count for a transcript is significantly different or differentially expressed under the treatment condition, we need to do a differential count analysis for the data. This is analogous to the differential gene analysis explained in Chapter 5, Analyzing Microarray Data with R. We will do such an analysis using the edgeR package in this recipe.

Getting ready

We will need two R packages, namely, edgeR and goseq, for the recipe. In terms of dataset, we will demonstrate in terms of the default data for these packages. The data comes from an experiment that examined the effect of androgen stimulation on a human prostate cancer cell line, LNCaP. The data has four control and ...

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