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.
Question: Methylation and RNA seq data
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ramyar.molania • 0 wrote:
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Devon Ryan ♦ 98k wrote:
"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.
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