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| -rw-r--r-- | topics/quality-control/shapiro-wilk-test.gmi | 33 |
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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 +``` |