Just wondering if anyone has any suggestions on how to normalize a dataset consisting of multiple sources of samples.
The samples are all from the same tissue type, and ran on the 450k array.
I have raw idats for 3 datasets, and only meth/unmeth intensities for the 4th dataset. Specifically I was wondering if it would be kosher to do ssNoob on the 3 datasets that I have idats for, because it makes sense to do background correction if possible, and then use quantile or BMIQ on the combined dataset to normalize everything together. Does this make sense?