[R] How to use Cox PH model to select genes from DNA gene expression profiles?

Jerome Asselin jerome at hivnet.ubc.ca
Wed Feb 19 00:40:05 CET 2003

See the "newdata" argument in ?survfit.

You can use it like this:
cox.surv <- survfit(cox.fit,newdata=selected.genes)
Indeed, you're going to have to build the data frame of your selected genes.

Then see ?plot.survfit for additional plotting options. That'll help you to 
build a "plot(cox.surv,--other arguments--)" command to draw nice survival 

Hope this helps.


On Tuesday 18 February 2003 15:04, Song, Guangchun wrote:
> Content-Length: 355
> Status: R
> X-Status: N
> I'm doing prediction of the survival cases using gene expression
> profiles(Affymetrix chips).  Can somebody tell me how to use the Cox PH
> model to select genes and make a prediction of survival?
> Thanks.
> Guangchun
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> http://www.stat.math.ethz.ch/mailman/listinfo/r-help


Jerome Asselin (Jérôme)
Statistical Analyst
British Columbia Centre for Excellence in HIV/AIDS
St. Paul's Hospital
608 - 1081 Burrard Street
Vancouver, British Columbia

Email: jerome at hivnet.ubc.ca
Phone: 604 806-9112   Fax: 604 806-9044

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