I got some methylation data from collaborators, and the initial goal is to estimate gender of subjects. I ran the data through Genome Studio and exported beta values, which I want to "feed" to minfi package.
Here is the problem, when I try to initialize MethylSet, using the matrix of beta values as "Meth", it complains that assays must have the same nrow and ncol (probably, not liking the absense of "Unmeth").
There is some problem with the sample sheet, so I would prefer to go with the Genome Studio output and the tutorial says "It is possible to use Genome Studio files together with the data structures contained in this package", but I do not see how I can do this.
I can also export intensities, that would be closer to what the help for MethylSet says about values between 0 and infinity, but this would not help with assays not having same nrow and ncol.
Anybody have any suggestions? Thank you