From 75314d83401e2def6c3731c30507ceeee1cb61bf Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 16 Aug 2024 11:37:04 +0200
Subject: Closed issue on gemma2 <-> R/qtl2 differences

---
 issues/gemma/gemma2-has-different-output-from-rqtl2.gmi | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

(limited to 'issues/gemma/gemma2-has-different-output-from-rqtl2.gmi')

diff --git a/issues/gemma/gemma2-has-different-output-from-rqtl2.gmi b/issues/gemma/gemma2-has-different-output-from-rqtl2.gmi
index 0f33b8e..5f04c82 100644
--- a/issues/gemma/gemma2-has-different-output-from-rqtl2.gmi
+++ b/issues/gemma/gemma2-has-different-output-from-rqtl2.gmi
@@ -5,7 +5,7 @@
 * assigned: pjotrp, davea
 * priority: high
 * type: bug, enhancement
-* status: unclear
+* status: closed
 * keywords: database, gemma, reaper, rqtl2
 
 # Description
@@ -74,3 +74,7 @@ Warning messages:
 ```
 
 The first warning matches above. If data is missing it may be filtered out. We'll have to check for that. The third warning I am not sure about. Probably a ranking of markers.
+
+# Conclusion
+
+It turned out that R/qtl was running HK - so it was a QTL mapping rather than an LMM.
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