RNA seq analysis in R

Question

[anasjamshed]

I have gene expression data from mice, and I want to apply wald test on each dds to compare:

Day 0

1. Control vs low
2. Control vs high
3. High vs low

Day 1

1. Control vs low
2. Control vs high
3. High vs low

Day 3

1. Control vs low
2. Control vs high
3. High vs low

Day 7

1. Control vs low
2. Control vs high
3. High vs low

I already find signficant genes of each condition but the problem is that can I make pca and heatmap of each condition?

[jared.andrews07]

Yes? Just limit the samples to those in the comparison of interest. Not sure what the question really is.