I have dataframe data
with columns like FollowUpDays, patient_vital_status and high, low information of a gene.
I'm trying to do survival analysis using the Followup information, patient_vital_status and the information of gene. I'm using like below:
surv_diff <- survdiff(Surv(FollowUpDays, patient_vital_status) ~ ENSG00000001460,
data = data)
surv_diff
Call:
survdiff(formula = Surv(FollowUpDays, patient_vital_status) ~
ENSG00000001460, data = data)
N Observed Expected (O-E)^2/E (O-E)^2/V
ENSG00000001460=high 332 57 70.5 2.58 5.99
ENSG00000001460=low 264 67 53.5 3.40 5.99
Chisq= 6 on 1 degrees of freedom, p= 0.01
From the above I could say that log rank test for difference in survival gives a p-value of p = 0.01, indicating that the Expression groups high and low differ significantly in survival.
To check the median of both the groups which tells us which group is good or bad for prognosis, I used like below:
library(survival)
fit <- survfit(Surv(FollowUpDays, patient_vital_status) ~ ENSG00000001460,
data = data)
print(fit)
Call: survfit(formula = Surv(FollowUpDays, patient_vital_status) ~
ENSG00000001460, data = data)
n events median 0.95LCL 0.95UCL
ENSG00000001460=high 332 57 NA 2134 NA
ENSG00000001460=low 264 67 1741 1503 NA
From the above I see that median of high group is NA
and 0.95UCL is also NA
for both the groups.
If the median of one of the group is NA
how can I say which group is worse for prognosis? Can anyone tell about these NA's
here.
Any help is appreciated. thanq
Thanq. I did the plot and I could see median for low group, but no median for high group. The plot looks like this I actually want to know which group is worse or good for prognosis without plotting. If there is a group (high or low) with median
NA
does it mean that group is good for prognosis?You don't have enough data for the red curve to reach 0.5 so the median can't be estimated. All you can say in that case is that it is greater than the last point you have.