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!

Your DESeqTransform object acts just like a data.frame when using the [ function, so you can just subset to the samples you want. As an example, using example data:

> library(DESeq2)
> example(results)
> vsd <- varianceStabilizingTransformation(dds)
> plotPCA(vsd)
## now just two of the genotypes
> plotPCA(vsd[,colData(vsd)$genotype %in% c("I", "III")])