Hi all,
I was just making some PCAs and I noticed that the plotPCA function within DESeq2 only takes the 500 genes with the highest variance. I was wondering if anyone knows what is the justification for this? vs taking the whole dataset? Is it just an attempt to filter out noise?
I'm working on a mouse RNA-Seq dataset at the moment and the plots look quite different if I take 500 genes vs taking 1000 genes
I was just making some PCAs and I noticed that the plotPCA function within DESeq2 only takes the 500 genes with the highest variance. I was wondering if anyone knows what is the justification for this? vs taking the whole dataset? Is it just an attempt to filter out noise?
I'm working on a mouse RNA-Seq dataset at the moment and the plots look quite different if I take 500 genes vs taking 1000 genes