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| author | Pjotr Prins | 2021-08-16 10:52:18 +0200 |
|---|---|---|
| committer | Pjotr Prins | 2021-08-16 10:52:18 +0200 |
| commit | 68b4a9ae8f341f803ac2ed0f758345b5ba90b456 (patch) | |
| tree | 80a8a75bda343d11cbb618954e0c5f6d65e24162 | |
| parent | bece7b48c12379f3ac2ea9c6f67a145f47d17c8d (diff) | |
| download | gn-gemtext-68b4a9ae8f341f803ac2ed0f758345b5ba90b456.tar.gz | |
gemma: add info by author of issue
| -rw-r--r-- | issues/gemma/multivariate_gemma_hangs-issue243.gmi | 9 |
1 files changed, 9 insertions, 0 deletions
diff --git a/issues/gemma/multivariate_gemma_hangs-issue243.gmi b/issues/gemma/multivariate_gemma_hangs-issue243.gmi index b5f07b2..c4f6874 100644 --- a/issues/gemma/multivariate_gemma_hangs-issue243.gmi +++ b/issues/gemma/multivariate_gemma_hangs-issue243.gmi @@ -2,6 +2,15 @@ => https://github.com/genetics-statistics/GEMMA/issues/243 +The simulated dataset was generated. Benjamin Chu writes: I think the main problem might be how I did the simulation. I believe it was something like + +``` +b ~ N(0, 1) # for k position of b only, others are 0 +yi ~ N(xi^T * b, 1) +``` + +where yi is length 2 vector of phenotype, xi is length 10000 genotype vector (entries 0, 1 or 2), and b is length 10000 effect size vector but only k position of b is drawn from standard Normal. This might be a poor simulation model for GEMMA. Later I changed the simulation model and the divergence problem went away. + The following command finishes: ``` |