R help - Feb 2003 - How to use Cox PH model to select genes from DNA gene expression profiles?

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

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
curves.

Hope this helps.

Jerome

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
>
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> R-help at stat.math.ethz.ch mailing list
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-- 

Jerome Asselin (J?r?me)
Statistical Analyst
British Columbia Centre for Excellence in HIV/AIDS
St. Paul's Hospital
608 - 1081 Burrard Street
Vancouver, British Columbia
CANADA V6Z 1Y6

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