Survival Analysis - No(Non-Missing) Observations

Question

[moranr]

Hi,

I am having a problem with my code. I am working with 5 datasets, 4 of them work fine with my code, however one is throwing up an error.

I am trying to calculate survival on the dataset i.e. get Hazard Ratio and p- value..

heres my code:

create a matrix for survival output

genes in rows , HR and P in columns

survival_gse4573_matrix <- matrix(nrow=colNum,ncol=2)

colnames(survival_gse4573_matrix) <- c("HR","P")

rownames(survival_gse4573_matrix) <- colnames(current_study)

get survival time and censored survival time based on status binary

survival_cens <- datTraits$STATUS.0.alive..1.dead.[358:487]

survival_time <- as.numeric(datTraits$suvival..months)[358:487]

for(i in 1:dim(gse4573_di_matrix)[2]){

a <- coxph(Surv(survival_time,as.numeric(survival_cens)) ~ gse4573_di_matrix[,i])

coeffs <- coef(summary(a))

HR <- coeffs[,2]

pVal <- (coeffs[,5])

fill matrix with HR and P for each gene

survival_gse4573_matrix[i,2] <- pVal

survival_gse4573_matrix[i,1] <- HR }

and the error:

coxph(Surv(survival_time, as.numeric(survival_cens)) ~ gse4573_di_matrix[,1])

Error in coxph(Surv(survival_time,as.numeric(survival_cens)) ~ gse4573_di_matrix[, : No (non-missing) observations

In addition:

Warning message: In

max(event[who2]) : no non-missing arguments to max; returning -Inf

The survival_cens contains only "NAs" as there was no status data for this dataset, is this the problem? If so, is there a way of solving it ?

Thanks, R

[zx8754]

Is it because you are assigning it to survival_cens and survival_time, then in formula for coxph you are using survivalcens and survivaltime?

[moranr]

No that is justhow the error puts them up... Im almost sure its due to status being effectively empty

[Devon Ryan]

If survival_cens is all NAs, I'm not sure how you could hope to do the computation, the result would be unknowable.

Answer 1

[moranr]

For anyone Interested the problem was that i had to read the survival_cens using survival_cens<- (as.numeric(as.character survival_cens))