Dear All:
 
I have a question on using coxph for multiple genes:
 
I have written code to loop through all 22283 genes in the Hgu-133A and
apply coxph on survival data.
 
However, I don't know how to work with the result for each gene:
 
survtest<-coxph(Surv(pcc.primary.stg.3.cox[,'fup_interval'],pcc.primary.stg.
3.cox[,'endpoint'])~pcc.primary.stg.3.cox[,'geneid'],pcc.primary.stg.3.cox)
 
each time I tried to look at what is in survtest it gives me this:
 
============================================================================
==============
coxph(formula = Surv(pcc.primary.stg.3.cox[, "fup_interval"], 
    pcc.primary.stg.3.cox[, "endpoint"]) ~ pcc.primary.stg.3.cox[, 
    "208181_at"], data = pcc.primary.stg.3.cox)
 

                                      coef exp(coef) se(coef)     z      p
pcc.primary.stg.3.cox[, "208181_at"] -1.87     0.154    0.688 -2.72 0.0065
 
Likelihood ratio test=8.56  on 1 df, p=0.00343  n= 48
============================================================================
===============
 
What I wanted to do is to use a matrix to store each "survtest" result, but
it seems to me there is no data 
structure in R to store the result of coxph into a matrix. I got the
following code to calculate a P value 
based on "survtest"
=================================
z<-survtest$coefficients/sqrt(surv$var)
p<-2*(1-pnorm(abs(z)))
 
then, what is the P value thus calculated?
===========================================
The question I have are:
 
1. How do I access different parts of coxph result?
2. Is there a way to store multiple coxph results into a data structure that
can be efficiently accessed?
3. if I find a list of genes I am interested, are there efficient to plot
all of them based on the survial data?
 
Thanks
Hao Liu, Ph. D
 
 

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