Obtain genes in PC1 and PC2 from bulk RNA-seq using DESeq2

Question

[cengiz]

Hi everyone,

I'm a beginner to RNA-seq, have done a few courses and trying to figure my way around somethings. I have created a PCA by the following means and would like to know what genes are in the principle components;

autoplot(pcDat, data = sampleinfo, colour = "calcified" , shape = "calcified", size = 5, x = 4, y = 3)

I tried following the previous thread How to get genes that make up principal components and got stuck at point one, wherein i cant get passed the following error:

rv <- rowVars(assay(pcDat)) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘assay’ for signature ‘"prcomp", "missing"’

Any advice, or link to another thread for advice would be much appreciated! Many thanks, Cengiz

[Basti]

First I would like to precise that a principal component do not "contain" specific genes. All genes matter in a principal component but their relative contribution will be different. If I understand well your goal is to find the genes that contribute the most to separate your samples along your first principal components. To understand your question, we would need to know which code you ran to obtain your pcDat object. Did you use prcomp ?