[R] Cox model

From: Eleni Christodoulou <elenichri_at_gmail.com>
Date: Tue, 12 Feb 2008 15:35:54 +0200

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,

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