[R] ROC for threshold value, biometrics

[Frank E Harrell Jr]

myint.tin-tin-htar at jvr.ap-hop-paris.fr wrote:
> Hello,
> 
> I am just a beginner of R 1.9.0.
> I try to construct a predictive score for the development of liver
> cancer in cirrhotic patients. So dependant variable is binanry (cancer
> yes or no). Independant variables are biological data. The aim is to
> find out a cut-off value which differentiate (theoratically)  from
> normal to pathological state for each biological data.

A binary endpoing is not a good choice for this problem, as the time to 
diagnosis is very important.  Unless you only have a biopsy at a single 
fixed time (e.g., 5 years post study entry) it would be good to consider 
for example a Cox proportional hazards model.  And there are many 
reasons for not using a cutoff, as detailed in my book Regression 
Modeling Strategies.


> 
> How can I step in procedue to get a cut-off value (threshold) for each
> variable? I think I should try by ROC. But I'm not sure. If so, someone
> can lead me?

Besides not recommending the use of cutoffs on an overall predicted 
value, I think that using cutoffs based on separate analyses of 
predictors is even worse.

Frank

> If not, someone can advice me how ?
> 
> Any advice will be cordially aprreciated.
> 
> Tin Tin Htar Myint
> Research assistant
> Liver unit
> Jean Verdier Hospital, Bondy
> France
> 
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-- 
Frank E Harrell Jr   Professor and Chair           School of Medicine
                      Department of Biostatistics   Vanderbilt University