Hi, when I run the code "myNorm_2<- champ.norm(beta=myLoad$beta[,1:2],arraytype="EPIC",method='BMIQ',cores=8,plotBMIQ = FALSE)"

head(myNorm_2) control A cg07881041 0.92852619 0.94222568 cg03513874 0.49956087 0.53085644 cg05451842 0.05017094 0.03743320 cg14797042 0.87706302 0.89601169 cg09838562 0.02482347 0.03169958 cg25458538 0.93871380 0.93427186

,and then I run the same code "myNorm22<- champ.norm(beta=myLoad$beta[,1:2],arraytype="EPIC",method='BMIQ',cores=8,plotBMIQ = FALSE)"

head(myNorm22) control A cg07881041 0.92937235 0.94192405 cg03513874 0.51218840 0.53629882 cg05451842 0.05584129 0.04034724 cg14797042 0.87897328 0.89552295 cg09838562 0.02666295 0.03414147 cg25458538 0.93929515 0.93373368

packageVersion("ChAMP") [1] '2.14.0'

I found the result is different. Why? Is it normal? Thanks!

Hi:

That’s because BMIQ method has some random sample process. There would be some difference, but in general they are very similar

You can use below code download the latest version from my Github, I have added some code to make the result exactly the same. I will also modify it in next version.

git clone https://github.com/YuanTian1991/ChAMP.git R CMD INSTALL ChAMP Best Tian