Hello,

I would like to ask whether I can use DEseq2 for the analysis of total RNA as group 1 and RNA from riboprotein IP as group 2, both from the same condition. I am interested in finding genes that are enriched in the IP.

Thank you,

Raya

I've typically seen DESeq2 used when comparing ratios of IP/total across treatments, using a design with an interaction term.

But I suppose you could also compare ribo IP / total for a single group. Do you only have single samples? If so, you should read the "Experiments without replicates" section of ?DESeq.

Thank you very much for you quick answer.

I have 3 replicates.

Raya