Re: [R] Capturing coxph warnings and errors

From: Stephen Weigand <weigand.stephen_at_gmail.com>
Date: Tue, 17 Jun 2008 21:07:17 -0500

On Tue, Jun 17, 2008 at 9:47 AM, Daniel Brewer <daniel.brewer_at_icr.ac.uk> wrote:
> 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?
>

Perhaps look at try() and look at the help for options() which explains different ways to handle warnings and errors.



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