I am a master student, I am new to the field and I have many difficulties. I am currently trying to identify the most methylated sites of tumor samples and normal TCGA-GBM tissue. However, when I use the get.diff.meth function from the ELMER package, I get 0 relevant probes and this is due to the fact that I only have 1 sample of normal solid tissue. I was told to add GBM normal samples from GEO. However, I already downloaded the data, but my question is: How do I gather the DNA methylation data from GEO and TCGA into a single variable to use the get.diff.meth function.
Thank you very much.