Question: Interpreting the output of score test using GENESIS
0
gravatar for lassana.a.samarakoon
13 days ago by
lassana.a.samarakoon0 wrote:

Hi all, I have output from an association test, using a Score test, from GENESIS software. My output has the following variables: Score Var Score.Stat Score.Val

According the GENESIS manual, I was expecting “Score.SE” and not “Var” variable. I want to confirm if the “Var” is Variance? If so, can I use √Var/√n to calculate the SE?

I really appreciate your help.

output score genesis • 52 views
ADD COMMENTlink modified 13 days ago by Stephanie M. Gogarten720 • written 13 days ago by lassana.a.samarakoon0
Answer: Interpreting the output of score test using GENESIS
2
gravatar for Stephanie M. Gogarten
13 days ago by
University of Washington
Stephanie M. Gogarten720 wrote:

You must be using an old version of GENESIS, but looking at the manual for the current version. Var is indeed the variance, and Score.SE = sqrt(Var) (no factor of n).

ADD COMMENTlink written 13 days ago by Stephanie M. Gogarten720

Thanks so much, Stephanie!

ADD REPLYlink written 13 days ago by lassana.a.samarakoon0

Hi, Is there anyway to convert the Beta estimate to a z-score here (equivalent to Score.Stat)?

ADD REPLYlink written 13 days ago by lassana.a.samarakoon0

I'm not entirely sure what you're asking here, since the Score test doesn't give a beta estimate. Is this what you're looking for? https://support.bioconductor.org/p/119621/

ADD REPLYlink written 13 days ago by Stephanie M. Gogarten720

Hi Stephanie, I'm so sorry for the confusion. I want to do the opposite of the above link you sent. 1)I want to convert the beta estimates to get a z score?

2) I want to know what is the z score variable of the assoc test output, is it "Score" or "Score.Stat"?

Thanks so much for your help.

ADD REPLYlink written 13 days ago by lassana.a.samarakoon0
1

1) The score test does not return a beta estimate, but you can get a good approximation of beta by taking Score/Score.SE^2); or, in your case, by taking Score/Var

2) Score.Stat is the test statistic, which is what you are thinking of when you say "z score variable". The current version of GENESIS returns a Score.Stat that is approximately Normally distributed (i.e. a z score); however, since you are using an old version of GENESIS, I can't remember if it returns that, or the square of that, which would follow a chi-square distribution with 1 d.f. To double check, the "z score" test statistic can be calculated as Score/Score.SE (or in your case Score/sqrt(Var)).

ADD REPLYlink modified 12 days ago • written 12 days ago by mconomos40
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