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, <[EMAIL PROTECTED]> 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@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@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. > [[alternative HTML version deleted]] ______________________________________________ R-help@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.
