S4 classes, exercises

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data("airway_small")

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#airway_small

1. Extract genes with exons overlapping the region 16:80000103-81066719

2. Calculate the mean counts for these rows

3. Exclude the last sample

4. Use the dds object from previously

5. Find the rows, where the gene expression is 0 for all the samples

6. Exclude these rows.

7. Run the analysis again on this subset

8. Using the DeSeq2 vignette, find out how to do a PCA on the gene expression data. Tip: you will have to apply a variance stabilizing transformation on the count data.