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Question: Methylation and RNA seq data
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gravatar for ramyar.molania
5.0 years ago by
ramyar.molania • 0
Australia
ramyar.molania • 0 wrote:

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.   
rna-seq methylation • 3.1k views
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modified 4.2 years ago • written 5.0 years ago by ramyar.molania • 0
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gravatar for Devon Ryan
5.0 years ago by
Devon Ryan ♦ 92k
Freiburg, Germany
Devon Ryan ♦ 92k 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.
ADD COMMENT • link written 5.0 years ago by Devon Ryan ♦ 92k
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