I am trying to understand the following DESeq PCA code:
plotPCA(vsd, intgroup = "condition", ntop = 500)
VERY different to the differentially expressed subset of genes from here:
de <- rownames(res[res$padj<0.05 & !is.na(res$padj), ]) plotPCA(vsd[de,], intgroup = "condition", ntop = 500)
What are thos ntop=500 selected at the beginning then? based on what are they TOP?