Re: [R] Cox model

From: <darteta001_at_ikasle.ehu.es>
Date: Tue, 12 Feb 2008 15:54:45 +0100 (CET)

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]]
>
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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 12 Feb 2008 - 15:19:21 GMT

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