I'm trying to run an analysis on methylation percentage using the multtest package, but I'm running into a problem.
I have a matrix where each columns is a subject, and each row is a number between 0-100, corresponding to percentage of methylation at that specific loci on the genome. Further, i have a vector containing the groups coding, so '0' represent a control and '1' a case.
I'm trying to run a t-test between the two groups (cases and controls) using the mt.maxT function, and while I'm getting the t-values and raw-p-values, all of the values in the adjusted p-value (adjp) are 1.
I'm trying to run the function as so:
mt.maxT(methyl.matrix, coding_groups, test = "t", side ="abs", fixed.seed.sampling = "y", B = 1000)
I've tried to run the raw p-values through the mt.rawp2adjp function, but then I'm getting an adjusted p list of 1s and 0s.
Furthermore, when trying to run the analysis using the MTP function, i'm getting this error:
Only one unique value in bootstrap sample for first group. Cannot calculate variance. This problem may be resolved if you try again with a different seed.
This error remains even after removing all missing (NA) values list-wise.
Any help will be appreciated,