Using DEseq with IP vs. total RNA
2
0
Entering edit mode
raya.fai ▴ 60
@rayafai-9396
Last seen 12 months ago
Israel

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

IP deseq2 • 1.3k views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 6 hours ago
United States

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.

ADD COMMENT
0
Entering edit mode
raya.fai ▴ 60
@rayafai-9396
Last seen 12 months ago
Israel

Thank you very much for you quick answer.

I have 3 replicates.

Raya

ADD COMMENT

Login before adding your answer.

Traffic: 806 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6