Preparing your data
We’ll be using the RNA-Seq differential expression results you generated earlier.
These will be in a file called ‘DE_genes_Basal_cells_Vs_Differentiated_cells.csv’ in the ‘Table' output folder from earlier. This file contains a list of differentially expressed genes that you generated using DESeq2. This list of DE genes will be used as input for functional annotation.
a. In windows explorer, go to: H:\workshop\RNAseq
b. In this folder, create a new folder called ‘functional_annotation’ (case-sensitive)
c. Open RStudio and create a new R script (‘File’ → “New File” → “R script”). Now hit ‘File’ → ‘Save’ and save the script in the H:\workshop\RNAseq\functional_annotation folder you created. Save the script file as ‘functional_annotation.R’
In the following sections, you will be copying and running the R code into your functional_annotation.R script.