# Databases Getting Out of Wack

## Tags

* assigned: Bonface, Zach, jgart
* priority: high
* type: bug
* 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 
> 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 
> 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 
> immediately after an update.

> The main thing I'm uncertain how to do (though I know is possible since Bonface already
> did something like this with GEMMA) is making the code run in the background after an
> update. It's probably more simple than I'm thinking, though.

Pjotr:
> Current qtlreaper runs in one of Arthur's scripts globally.

> When we recompute on uploading the data we can use GEMMA. That is the
> plan. But let the team do qtlreaper first. Don't want too many moving parts.

Rob:
> Yes, that and more. These values are displayed in search results and used
> to sort by expression mean and peak LRS (using pathetically old code and
> genotypes). Now if GEMMA were wicked fast we could recompute the 60 million
> 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.