Question

how to detect association between SNP and expression?

0

Entering edit mode

5.5 years ago

hxlei613 ▴ 100

Hi, I want to find the association between SNP and expression in normal CD4+. However I only have 18 samples. If I have hundreds of samples I can do eQTL analysis. What can I do in this situation ? I haven't find any solution yet. Glad for any suggestion. Thanks.

SNP expression association • 1.0k views

ADD COMMENT • link updated 5.5 years ago by Dhana ▴ 110 • written 5.5 years ago by hxlei613 ▴ 100

score 0 · Answer 1 · 2018-10-12

It is still possible to do eQTL analysis with 18 samples, you can try using the Matrix eQTL package. I have used it previously and found it to be very simple and efficient. In case you do not find any eQTLs in it might be good to try other non-parametric tests such as Kruskal-Wallis and plot the results to see if there is a linear trend.