From ba56073820818a8edc198c823b016248fde2c244 Mon Sep 17 00:00:00 2001
From: jgart
Date: Wed, 24 Nov 2021 01:26:26 -0500
Subject: Move Shapiro-Wilk test to separate file

---
 topics/quality-control/shapiro-wilk-test.gmi | 33 ++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)
 create mode 100644 topics/quality-control/shapiro-wilk-test.gmi

(limited to 'topics/quality-control/shapiro-wilk-test.gmi')

diff --git a/topics/quality-control/shapiro-wilk-test.gmi b/topics/quality-control/shapiro-wilk-test.gmi
new file mode 100644
index 0000000..b1bdbfd
--- /dev/null
+++ b/topics/quality-control/shapiro-wilk-test.gmi
@@ -0,0 +1,33 @@
+# Shapiro Wilk Test
+
+This document contains more info about QC step 11.
+
+https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.shapiro.html
+https://vedexcel.com/how-to-perform-a-shapiro-wilk-test-in-python/
+
+```
+Here is a simple QC procedure we may want to consider that was used by
+Megan and Camron in a recent paper  that I have attached.
+
+
+Phenotypes were assessed for normality using the Shapiro–Wilk Test. Because
+some of the data residuals devi- ated significantly from normality, we used
+the orderNorm function to perform Ordered Quantile normalization43 on all
+phenotypes.
+
+--
+Rob
+```
+
+```
+QTL analysis was performed in F2 mice using the R package R/qtl
+(RRID:SCR_009085) as previously described.11,29,42 Quality checking
+of genotypes and QTL analysis were performed in R (https://www.r-
+project.org/) using R/bestNormalize (https://github.com/petersonR/
+bestNormalize) and R/qtl.42 Phenotypes were assessed for normality
+using the Shapiro–Wilk Test. Because some of the data residuals devi-
+ated significantly from normality, we used the orderNorm function to
+perform Ordered Quantile normalization43 on all phenotypes. QTL
+--
+A quantitative trait variant in Gabra2 underlies increased methamphetamine stimulant sensitivity
+```
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