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| author | Pjotr Prins | 2023-03-16 12:08:59 +0100 |
|---|---|---|
| committer | Pjotr Prins | 2023-03-16 12:08:59 +0100 |
| commit | 71a4fb1dacc5c68c42694907a218f6f763f29762 (patch) | |
| tree | 3f2c9f5afd8bc5da761962f5a97003f3b6b8597a /issues/gemma/databases-getting-out-of-wack.gmi | |
| parent | 81c7e75c5f94d3fa9efd31c398731a4848549da1 (diff) | |
| download | gn-gemtext-71a4fb1dacc5c68c42694907a218f6f763f29762.tar.gz | |
Starting on gemma precompute
Diffstat (limited to 'issues/gemma/databases-getting-out-of-wack.gmi')
| -rw-r--r-- | issues/gemma/databases-getting-out-of-wack.gmi | 25 |
1 files changed, 15 insertions, 10 deletions
diff --git a/issues/gemma/databases-getting-out-of-wack.gmi b/issues/gemma/databases-getting-out-of-wack.gmi index a102846..45aa6c9 100644 --- a/issues/gemma/databases-getting-out-of-wack.gmi +++ b/issues/gemma/databases-getting-out-of-wack.gmi @@ -1,25 +1,33 @@ # Databases Getting Out of Wack +This issue refers to precomputed scores generated by the ancient reaper module that runs as a script: + +=> https://github.com/genenetwork/genenetwork2/blob/testing/scripts/maintenance/QTL_Reaper_v6.py + +We'll create a new issue: + +=> lmm-precomputed-scores.gmi + ## Tags -* assigned: Bonface, Zach, jgart +* assigned: pjotrp * priority: high -* type: bug +* type: bug, enhancement * status: unclear * keywords: database, gemma, reaper ## Let's use Gemma instead of Reaper Zachary: -> If we're using GEMMA, we'll need to recalculate all other trait Max LRS scores using -> GEMMA as well (so I think we should just do this with qtlreaper for now). Otherwise +> If we're using GEMMA, we'll need to recalculate all other trait Max LRS scores using +> GEMMA as well (so I think we should just do this with qtlreaper for now). Otherwise > we'll just have a bunch of qtlreaper scores mixed with GEMMA scores without the user -> having any way of knowing the difference. Also, storing the full results (what Rob -> calls the "full vector model") will require some sort of fundamental change to the +> having any way of knowing the difference. Also, storing the full results (what Rob +> calls the "full vector model") will require some sort of fundamental change to the > way we store this data and should be postponed for later (since the high priority > immediate issue is to ensure that the stored Max LRS values aren't wrong) -> As for Mean, that should be simple, since it's just taking the average of sample values +> As for Mean, that should be simple, since it's just taking the average of sample values > immediately after an update. > The main thing I'm uncertain how to do (though I know is possible since Bonface already @@ -39,6 +47,3 @@ Rob: > BXD vector results and store that as a big juicy TRANSFORMATIVE blob of > data. A big paper in doing just that. Reaper is just wrong at this > point. We have LMM: We should use it. - - - |