Hao, I'm not sure but you have specified your modell as tautology. The formula below should be enough:
survtest <- coxph(Surv(fup_interval, endpoint) ~ geneid, data = pcc.primary.stg.3.cox) HTH Fredrik ----- Original Message ----- From: "Hao Liu" <[EMAIL PROTECTED]> To: <r-help@stat.math.ethz.ch> Sent: Tuesday, January 17, 2006 7:47 PM Subject: [R] help with parsing multiple coxph() results > 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 > > > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html > ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
