[R] Capturing coxph warnings and errors

Daniel Brewer daniel.brewer at icr.ac.uk
Tue Jun 17 16:47:40 CEST 2008


I have a script that takes a subset of genes on a microarray and tries
to fit a coxph model to the expression values for each gene.  This seems
to work fine but in some cases it produces warnings and/or errors.

For example:
Error in fitter(X, Y, strats, offset, init, control, weights = weights,  :
  NA/NaN/Inf in foreign function call (arg 6)
In addition: Warning message:
In fitter(X, Y, strats, offset, init, control, weights = weights,  :
  Ran out of iterations and did not converge

In this situation I would like to:
1) Deal with it so that it the scripts result data.frame the p value etc
are set to NA.
2) Suppress the Error and Warning messages

What is the best way to do this?


Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
Email: daniel.brewer at icr.ac.uk

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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