"I had planned to carry out 450K human methylation data analysis and gene expression analysis to corelate differentially expressed genes to differentially methylated regions for publicly available cancer data from TCGA."
I had used COHCAP to find DMRs in 75 samples (65 T + 10 N).[450 K human methylation data level 1 tcga]
Next I used edgeR to find differentially expressed genes in 68 samples (65T + 3N) (rnaseq data was missing for 7 N samples) [rnaseqv2 data level3 tcga]
For a proof of concept, I extracted 458 genes from CpG_island_filtered-Avg-by_Island.xlsx (from COHCAP analysis)
and only 36 downregulated genes from edgeR analysis.
Only 2 genes were common in both the lists. I am worried if I am missing some important steps as I had expected at least 20 - 30 genes that would be commonly related in both the COHCAP analysis(450K methylation array level 1) and edgeR analysis (rnaseqv2 level 3).
Any suggestions or improvements are welcome!