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Question: TCGA survival analysis with z-scores all samples altered
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gravatar for TriS
5.8 years ago by
TriS • 4.2k
United States, Buffalo
TriS • 4.2k wrote:

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: http://bioinformatics.mdanderson.org/Supplements/ResidualDisease/Reports/osCurves.html

...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?!
survival rna-seq kaplan-meier tcga • 4.7k views
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modified 4.2 years ago by ahnksmd • 0 • written 5.8 years ago by TriS • 4.2k
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gravatar for ahnksmd
4.2 years ago by
ahnksmd • 0
ahnksmd • 0 wrote:

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
ADD COMMENT • link written 4.2 years ago by ahnksmd • 0
1

follow this link

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

ADD REPLY • link written 4.2 years ago by Mike • 1.6k

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?

ADD REPLY • link written 4.2 years ago by ahnksmd • 0

you can do the following:

z = [(value gene X in tumor Y)-(mean gene X in tumor)]/(standard deviation X in tumor)
ADD REPLY • link written 4.1 years ago by TriS • 4.2k
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