[R] Capturing coxph warnings and errors

From: Daniel Brewer <daniel.brewer_at_icr.ac.uk>
Date: Tue, 17 Jun 2008 15:47:40 +0100


Hi,

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?

Thanks

-- 

**************************************************************
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. This e-mail message is confidential and for use by the a...{{dropped:2}} ______________________________________________ R-help_at_r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Received on Tue 17 Jun 2008 - 15:37:35 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Wed 18 Jun 2008 - 03:31:01 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.

list of date sections of archive