TCGA survival analysis with z-scores all samples altered

Question

[TriS]

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?!

Answer 1

[ahnksmd]

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

[Mike]

follow this link

Survival analysis of TCGA patients integrating gene expression (RNASeq) data

[ahnksmd]

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?

[TriS]

you can do the following:

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