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.
"Is it true?" Well it's your workflow, so you'd have to tell us whether what you described accurately represents what you're doing or not.
Presumably you meant, "is this a good way to do it?" My only critique is that you might want to use M-values, since they won't have the ceiling/floor effects. You might also want to stratify things by high/low/medium promoter CpG density. I've also seen people divide things into <20% CpG, 20 to <40% CpG and so on groups. Maybe that's worthwhile, maybe not (there's no best practice here yet), but it's something to keep in mind.