Hi there. i'm analyzing a HM450K array methylation data with 2 groups(patients vs healthy controls). I wanna to compare the two groups in order to find differentially methylated probes(DMPs), so, I ran limma analysis on this dataset. But when i discuss the pipeline with someone who engages in methylation data analysis in a bioinfo company, he told me that he add the MDS1, MDS2 from multidimensional scaling as covariates in find DMPs. He thought it can adjust the potential for population stratification in methylation data. However, some previous studies use the MDS or PCA plot to testify whether methylation data can provide strong signatures to the target condition. So I worry about adding the MDS1, MDS2 as covariates may decrease the difference between patients and controls. Due to time constraints, more precisely were not discussed in depth.
So, i still confused about this question. Hope to have an expert can answer. Any suggestion will be great appreciated!
