Question: What is the cutoff used for define high or low expression level of gene for survival analysis
gravatar for mygamefun3
8 weeks ago by
mygamefun30 wrote:

Hi everyone

In RNA-seq analysis, we need to separate samples into two groups for survival analysis. How can I define high level or low level for a gene according to counts or FPKM. Use median? average or quantile?

In TCGA or Oncomine, how are they define the cutoff for a gene ?


rna-seq • 227 views
ADD COMMENTlink written 8 weeks ago by mygamefun30

There's no definitive answer to your question. I would not advise going by the median or average. Quantile is a reasonable idea, or tertiles, with the higher third being regarded as "high expression".

An even better idea would be to convert your data to the Z scale, i.e., standard deviations from the mean, and then choose absolute 3, 4, 5, or 6 (3, 4, 5, or 6 standard deviations from the mean) as potential cut-offs. I trust that you have QC'd your data already and that low count transcripts have been removed.

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by Kevin Blighe14k

Thanks for your advice.

ADD REPLYlink written 8 weeks ago by mygamefun30
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