TCGA survival analysis with z-scores all samples altered
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6.5 years ago
TriS ★ 4.3k

Hi all

I'm trying to do my own survival analysis with TCGA clinical data for PRAD in the following way:

  • downloaded latest RNASeq V2 RSEM normalized for all samples
  • calculated z-scores as z = (expression in tumor sample) - (mean expression in diploid samples) / (standard deviation of expression in diploid samples)
  • downloaded latest clinical data
  • followed "tutorial" here

...however, using a threshold of +/- 1.96 for zscores, which should correspond to a p = 0.05, I have all the tumor samples that present at least one alteration in my gene signature...this means that I cannot really build a kaplain meier plot of altered vs non-altered samples...

How would you handle this situation?!

kaplan-meier RNA-Seq TCGA survival • 5.0k views
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4.8 years ago
ahnksmd • 0

Hi, TriS

I also encounter same problem, all of my samples are tumor. Did you resolve this problem and if so, please let me know.

Thank you
Keunsuu

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Thank you.

This link seems that z score was calculated between tumor and normal samples.

When I have just tumor samples, how can I do?

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you can do the following:

z = [(value gene X in tumor Y)-(mean gene X in tumor)]/(standard deviation X in tumor)
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