There are actually two questions.
1) I am using the ComBat function in sva package to adjust for batch effect (plate). Before adjusting, the beta values range from 0.0016 to 0.9997. After adjusting, the beta values range from -0.4152 to 1.4015. What is the recommended way to deal with this? Should I just arbitrarily make all beta values smaller than 0 to 0, and all beta values larger than 1 to 1?
2) I am using the beta2m function in lumi package to convert beta values to M values. But when the beta value equal to 1, NaN is returned. Should I make all 1 to (1-0.00001) or something like this? But should I use 1-0.00001 or 1-0.001 or something else? Is there a guideline?
It would be best if anyone could also provide reference.