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authorjgart2021-11-24 00:05:03 -0500
committerjgart2021-11-24 00:30:02 -0500
commitf46ed96a01617514547da4636b6121fadc5f2326 (patch)
treefafbc3c3c879d78e4466cebc1830cf6b303307e5
parent9c6b56fafd8647a6ea4385e24b24d47ae2b975c9 (diff)
downloadgn-gemtext-f46ed96a01617514547da4636b6121fadc5f2326.tar.gz
Add Shapiro-Wilk Test QC Check
scipy has an implementation
-rw-r--r--topics/quality-control/qc-checks.gmi19
1 files changed, 19 insertions, 0 deletions
diff --git a/topics/quality-control/qc-checks.gmi b/topics/quality-control/qc-checks.gmi
index f2e47fd..30236e1 100644
--- a/topics/quality-control/qc-checks.gmi
+++ b/topics/quality-control/qc-checks.gmi
@@ -39,3 +39,22 @@ is allowed into the GeneNetwork will be 22,000 entries.
9. There should be no trailing spaces in data cells.
10. Entries should have the same capitalization style.
+
+11. Assesing Phenotypes for normality with Shapiro-Wilk Test.
+
+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
+```