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| author | jgart | 2021-11-24 00:05:03 -0500 |
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| committer | jgart | 2021-11-24 00:30:02 -0500 |
| commit | f46ed96a01617514547da4636b6121fadc5f2326 (patch) | |
| tree | fafbc3c3c879d78e4466cebc1830cf6b303307e5 | |
| parent | 9c6b56fafd8647a6ea4385e24b24d47ae2b975c9 (diff) | |
| download | gn-gemtext-f46ed96a01617514547da4636b6121fadc5f2326.tar.gz | |
Add Shapiro-Wilk Test QC Check
scipy has an implementation
| -rw-r--r-- | topics/quality-control/qc-checks.gmi | 19 |
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 +``` |