Closed DengEr-1993 closed 1 year ago
Hi @DengEr-1993,
Yes, correct. To modify the outcome of the p-value adjustment (q-value), simply change the adjust
parameter of the calculateDiffMeth
function. This should allow you to fine-tune the results and not change the reported methylation difference.
Best, Alex
Hello @alexg9010 ,
I have a small question about the
calculateDiffMeth()
function.I can get different results if I use different parameters in
calculateDiffMeth()
but I want to know if any parameters can only change the p value and q value but will not affect the meth.diff result ?
For exmaple, based on the scripts below, respectively :
myDiff_new = calculateDiffMeth(meth_new, overdispersion="MN", test="Chisq", num.cores = 10) or myDiff_new = calculateDiffMeth(meth_new, covariates = covariates, overdispersion="MN", test="Chisq", num.cores = 10)
how can I use other different paramters to change p value and q value but will not affect the meth.diff result of each line ?
I have confirmed that parameter "test=()" can change both values. Can
adjust=()
does it ?Best, Xiangyi