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Diffstat (limited to 'topics/quality-control/qc-checks.gmi')
| -rw-r--r-- | topics/quality-control/qc-checks.gmi | 30 |
1 files changed, 1 insertions, 29 deletions
diff --git a/topics/quality-control/qc-checks.gmi b/topics/quality-control/qc-checks.gmi index 713fa0b..149557c 100644 --- a/topics/quality-control/qc-checks.gmi +++ b/topics/quality-control/qc-checks.gmi @@ -42,32 +42,4 @@ is allowed into the GeneNetwork will be 22,000 entries. 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 -``` - -``` -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 -``` +12. Check for annotations file. |