how to detect association between SNP and expression?

Question

[hxlei613]

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.

Answer 1

[Dhana]

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.