**1.1k**wrote:

I wish to determine a significance threshold for a small eQTL study.

I computed p-values for the observed data under the model,

```
Y ~ A
```

where Y is gene expression and A is the snp.

I then generated a 1000 permutations of Y and recomputed the p-values. I wish to use these permutations to calculate a cut-off but am not at all certain how to go about it.

Any suggestions?

Thanks.

**70**• written 9.1 years ago by Darren J. Fitzpatrick •

**1.1k**