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I have a data set in which we are comparing RNA seq data collected from twelve different mouse strains. I have figured out how to run the DESeq2 analysis, but I want to compare two of the strains together with a PCA graph and maybe a heat map too. I am using vsd and ntd for the PCA but it just has too much information on the other strains. How would I compare just AJ vs B6?
plotPCA(vsd, intergroup=c("strain")
#this is the commard I am using is there a way to show only some of the data in the whole set?
Thanks in advance!