Re: [R] Cox model

From: Eleni Christodoulou <elenichri_at_gmail.com>
Date: Tue, 12 Feb 2008 17:02:25 +0200

Hi David,

The problem is that I need all these regressors. I need a coefficient for every one of them and then rank them according to that coefficient.

Thanks,
Eleni

On Feb 12, 2008 4:54 PM, <darteta001_at_ikasle.ehu.es> wrote:

> Hi Eleni,
>
> I am not an expert in R or statistics but in my opinion you have too
> many regressors compared to the number of observations and that might

> be the reason why you get the error. Others might say better but as
> far as I know, having only 80 observations, it is a good idea to first
> filter your list of variables down to a few tenths.
>
>
> HTH
>
> David
>
> > Hello R-community,
> >
> > It's been a week now that I am struggling with the implementation of
> a cox
> > model in R. I have 80 cancer patients, so 80 time measurements and 80
> > relapse or no measurements (respective to censor, 1 if relapsed over

> the
> > examined period, 0 if not). My microarray data contain around 18000
> genes.
> > So I have the expressions of 18000 genes in each of the 80 tumors
> (matrix
> > 80*18000). I would like to build a cox model in order to retrieve
> the most
> > significant genes (according to the p-value). The command that I am
> using
> > is:
> >
> > test1 <- list(time,relapse,genes)
> > coxph( Surv(time, relapse) ~ genes, test1)
> >
> > where time is a vector of size 80 containing the times, relapse is a
> vector
> > of size 80 containing the relapse values and genes is a matrix
> 80*18000.
> > When I give the coxph command I retrieve an error saying that cannot
> > allocate vector of size 2.7Mb (in Windows). I also tried linux and

> then I
> > receive error that maximum memory is reached. I increase the memory
> by
> > initializing R with the command:
> > R --min-vsize=10M --max-vsize=250M --min-nsize=1M --max-nsize=200M

> >
> > I think it cannot get better than that because if I try for example

> > max-vsize=300 the memomry capacity is stored as NA.
> >
> > Does anyone have any idea why this happens and how I can overcome it?
> >
> > I would be really grateful if you could help!
> > It has been bothering me a lot!
> >
> > Thank you all,
> > Eleni
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > 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.
> >
>
> ______________________________________________
> R-help_at_r-project.org mailing list
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> PLEASE do read the posting guide
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>

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