Hi,

I have 33 RNA-seq samples from two conditions which can be separated in other sub-conditions. I ran DESEq2 on all the dataset up to

rld <- rlog(dds, blind=FALSE)

Then, I would to run plotPCA into a subset of samples of each condition. Is this code right in order to do that ?

For the first condition :
plotPCA(rld[protein_coding_genes_id_vect,c(1,2,3,10,11,12,19,20,21,22,23,24,25,26,27,31,32,33)], intgroup=c("condition"))

For the second condition :

plotPCA(rld[protein_coding_genes_id_vect,c(4,5,6,7,8,9,13,14,15,16,17,18,28,29,30)], intgroup=c("condition"))

Thanks a lot for your answers !

Yes, you can subset the DESeqTransform object directly to perform PCA on subsets.