I have a set of different phenotypes which I want to use for a GWAS analysis (general linear model). I have a couple of questions and uncertainty about the phenotype data input.
- I have control and samples and usually we normalize all sample to the control for other calculations.
Mean control - 60%
Mean sample1 - 20 %
Mean sample1 normalized to control - 20*100/60 = 33,3 %
Is this normalization step correct for a GWAS analysis?
Should the phenotype data scaled into 0...1 range? I have different scales for different phenotypes but the results should be compared and compatible.
Some of my phenotypes are not normality distributed. What is the best way to handle such data? I have read that the data should be normally distributed for GWAS analysis.
Here are the histograms of two phenotypes: