Question: logrank test p-value comparing quantile intervals
0
gravatar for rbrtdambrosio
3.1 years ago by
rbrtdambrosio70 wrote:

Hello,

I'm using the FIREBROWSE platform and I'm trying to replicate the survival analysis described here:

http://gdac.broadinstitute.org/runs/analyses__2016_01_28/reports/cancer/COAD-TP/Correlate_Clinical_vs_mRNAseq/nozzle.html

In the description of the method used they reported: " logrank test in univariate Cox regression analysis with proportional hazards model was used to estimate the P values comparing quantile intervals using the 'coxph' function in R. Kaplan-Meier survival curves were plotted using quantile intervals at c(0, 0.25, 0.50, 0.75, 1). If there is only one interval group, it will not try survival analysis."

This description is not really clear to me. I know that I can estimate the logrank p-value using the coxph function, but I can't understand how they used the quantile intervals information.

Sorry if the question is trivial and thanks for your help.

survival rna-seq logrank cox R • 1.2k views
ADD COMMENTlink written 3.1 years ago by rbrtdambrosio70

I assume that they used the quantiles of each of their clinical features as the groups for the test.

ADD REPLYlink written 3.1 years ago by Devon Ryan92k

Thanks for the comment.

Since they are performing survival analysis looking, ad example, for the correlation with "time to death or last follow up", I've assumed that the grouping was given by the event ("death") of the patient.

My guess was that the quantile was computed on the output (score) of the cox model for each clinical feature. Doing so they define different groups for the Kaplan-Mayer curves from which compute the logrank. But also in this way is not clear how they compute the logrank for multiple curves.

ADD REPLYlink written 3.1 years ago by rbrtdambrosio70
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1550 users visited in the last hour