Question: TCGA survival analysis with z-scores all samples altered
0
gravatar for TriS
4.0 years ago by
TriS3.5k
United States, Buffalo
TriS3.5k 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?!

ADD COMMENTlink modified 2.4 years ago by ahnksmd0 • written 4.0 years ago by TriS3.5k
0
gravatar for ahnksmd
2.4 years ago by
ahnksmd0
ahnksmd0 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 COMMENTlink written 2.4 years ago by ahnksmd0
1

follow this link

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

ADD REPLYlink written 2.4 years ago by Mike1.1k

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 REPLYlink written 2.4 years ago by ahnksmd0

you can do the following:

z = [(value gene X in tumor Y)-(mean gene X in tumor)]/(standard deviation X in tumor)
ADD REPLYlink written 2.4 years ago by TriS3.5k
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