Hi,

I am currently carrying out an analysis on some 450k data to look for sub-grouping. My pipeline has been so far to preprocess the data in minfi and carry out an unsupervised clustering in NMF. With my ranks identified, I took the H values and correlated those to my M-values set. I now have a list of cgIDs which are correlated to the clusters and my next step would be to attach some functional annotation to the list.

What I would ideally like to do is map the individual probes or DMP/Rs to specific genes/promoters/enhancer regions. I do realise that probes do not recapitulate genes and have been advised to use DMRcate. I would however like to carry out some sort of GO analysis and I do potentially have RNASeq data available, but I would like to push my 450k data as far as I can in the first instance.

I am looking for advice on the next steps in the pipeline of my analysis or links to relevant literature as I am still new to R and bioconductor and I'm currently at a loss as to where to go with this.