I am conducting a survival analysis using the gene expression values (converted to z-scores) from a certain gene and event free survival time for 249 patients. I am a newbie to this, so please excuse my lack of expertise (this is also my second question on here, so sorry for any formatting errors, I'm still figuring this out).
Here is my code:
finaldata$SurvObj <- with(finaldata, Surv(efst, status == 2))
res.cox1 <- coxph(SurvObj ~ Zscore, data = finaldata)
And here is the output:
Call: coxph(formula = SurvObj ~ Zscore, data = finaldata) n= 247, number of events= 140 (2 observations deleted due to missingness) coef exp(coef) se(coef) z Pr(>|z|) Zscore 0.5878 1.8001 0.2118 2.776 0.0055 --- Signif. codes: 0 0.001 0.01 0.05 ‘.’ 0.1 ‘ ’ 1 exp(coef) exp(-coef) lower .95 upper .95 Zscore 1.8 0.5555 1.189 2.726 Concordance= 0.561 (se = 0.025 ) Likelihood ratio test= 7.92 on 1 df, p=0.005 Wald test = 7.71 on 1 df, p=0.006 Score (logrank) test = 7.74 on 1 df, p=0.005
efst is the event free survival time for patients, the status is whether they are dead or alive (1 is alive, 2 is dead), and Zscore is the Z-Score value for the expression of the gene in question for each of the patients (to understand whether the expression is relatively high or low).
However, I find it highly improbable that I am receiving such p-values and that leads me to think that I have definitely done something incorrectly since this is my first time trying this out.
Please let me know whether you are able to find any errors I have made/how to fix them, or any help at all with how to better interpret this data. I appreciate it!