Exercise

RNA-Seq DE workflow summary

NOTE: It may take a bit longer to load this exercise.

Let's run through the DESeq2 workflow using the full dataset with both wildtype and smoc2 overexpression samples included. We have loaded the DESeq2 and dplyr libraries and read in the metadata file, all_metadata and the raw counts file, all_rawcounts for you.

full metadata

Instructions

100 XP

Check that the samples are in the same order in both all_rawcounts and all_metadata using the rownames(), colnames(), all(), and %in% operator.
Create the DESeq2 object using the appropriate design, testing for the effect of condition while controlling for genotype.
Create the DESeq2 object using the appropriate design, controlling for genotype and condition individually, but test for genotype:condition.