Defining metagenes from NMF in methylation array data - next step?
0
0
Entering edit mode
@yuragrabovska-9835
Last seen 2.4 years ago
United Kingdom

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. 

NMF minfi • 1.1k views
ADD COMMENT

Login before adding your answer.

Traffic: 541 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6