[R] Survival Analysis Questions

[Lance Parsons]

I am currently using the coxph function from R on a microarray dataset. 
  The curve fit is performed using each gene's expression measurements 
separately.  I then get a p-value for each gene, from the Coxph.summary 
method.  Can someone please explain how this is computed and the 
significance of the p-value?

However, the bigger question I have is how to perform permutation tests 
to get a more robust estimate of significance.  After permuting the 
survival times and running Cox on each gene, I would like to save the 
most extreme values (representing the gene most correlated with 
survival).  After ~1000 runs, I then run Cox on each gene with the 
correct survival numbers.  My question is, which statistic(s) should I 
look at?  I was thinking that the coefficient might be appropriate, but 
I'm new to survival analysis and am not certain.  Can anyone offer any 
advice?

Finally, currently, I permute the survival times and maintain the proper 
association with the status column.  Should I permute the status separately?

Thanks for your time.