I am working on TCGA data for finding correlation between gene expression and methylation of a set of genes. I use level 3 of TCGA data for my analysis. I have extracted beta value of different 450k probes and RPKM values of RNA seq. For finding correlation of methylation and gene expression of my interest gene, I have done spearman test and calculated q value. This is my workflow.If my workflow needs further analysis I would be really appreciated if someone could guide me.