Hi again,

I am trying to create bootstrap samples of my training set and conduct a
univariate cox analysis on each of them. I tried both in Linux and windows.
After 17 samples in Linux and 8 in Windows the process is killed. Does
anyone know why this happens?

Thanks in advance,
Eleni

On Thu, Feb 14, 2008 at 1:10 PM, <J.J.Goeman@lumc.nl> wrote:

>  Dear Eleni,
>
> If you are interested in prediction of survival with (a subset of) your
> 18000 genes, you may want to have a look at the "penalized" package on CRAN
> (http://cran.us.r-project.org/src/contrib/Descriptions/penalized.html) or
> other packages there that do penalized estimation.
>
> Jelle
>
>
> > -----Original Message-----
> > From: Eleni Christodoulou [mailto:elenichri@gmail.com]
> > Sent: 13 February 2008 13:22
> > To: phguardiol@aol.com
> > Cc: rdiaz@cnio.es; bioconductor@stat.math.ethz.ch
> > Subject: Re: [BioC] Re : Cox Model
> >
> > Hi,
> >
> > Thanks for the replies. I will probably try to perform
> > survival analysis on each of the genes to get gene-wise
> > p-values and then select the most significant (the ones that
> > are below a certain p-value) and proceed to a full cox
> > regression using the significant genes. Do you think that
> > this makes sense?
> >
> > Thanks a lot,
> > Eleni
> >
> > On Feb 13, 2008 2:11 PM, <phguardiol@aol.com> wrote:
> >
> > >  Hi,
> > > wouldnt it make sense to first have data reduction dimensionality
> > > before undergoing such survival analysis ? Certainly, some of your
> > > genes have similar expression profiles across samples...?
> > >  Best,
> > >  Philippe Guardiola
> > >
> > >
> > >  -----E-mail d'origine-----
> > > De : Ramon Diaz-Uriarte <rdiaz@cnio.es> A :
> > > bioconductor@stat.math.ethz.ch Cc : Eleni Christodoulou
> > > <elenichri@gmail.com> Envoyé le : Me, 13 Février 2008 11:23 Sujet :
> > > Re: [BioC] Cox Model
> > >
> > >  Dear Eleni,
> > >
> > >
> > > You are trying to fit a model with 18000 covariates but only 80
> > > samples (of
> > >
> > > which, at most, only 80 are not censored). Just doing it
> > the way you
> > > are
> > >
> > > trying to do it is unlikely to work or make much sense...
> > >
> > >
> > > You might want to take a look at the work of Torsten Hothorn and
> > > colleagues on
> > >
> > > survival ensembles, with implementations in the R package
> > mboost, and
> > > their
> > >
> > > work on random forests for survival data (see R package
> > party). Some
> > > of this
> > >
> > > funcionality is also accessible through our web-based tool SignS
> > >
> > > (http://signs.bioinfo.cnio.es), which uses the above packages.
> > >
> > >
> > > Depending on your exact question, you might also want to
> > look at the
> > > approach
> > >
> > > of Jelle Goeman, for testing whether sets of genes (e.g.,
> > you complete
> > > 18000
> > >
> > > set of genes) are related to the outcome of interest
> > (survival in your case).
> > >
> > > Goeman's approach is available in the globaltest package from BioC.
> > >
> > >
> > > Hope this helps,
> > >
> > >
> > > R.
> > >
> > >
> > >
> > > On Wednesday 13 February 2008 08:10, Eleni Christodoulou wrote:
> > >
> > > > Hello BioC-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]]
> > >
> > > >
> > >
> > > > _______________________________________________
> > >
> > > > Bioconductor mailing list
> > >
> > > > Bioconductor@stat.math.ethz.ch
> > >
> > > > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > >
> > > > Search the archives:
> > >
> > > > http://news.gmane.org/gmane.science.biology.informatics.conductor
> > >
> > >
> > > --
> > >
> > > Ramón Díaz-Uriarte
> > >
> > > Statistical Computing Team
> > >
> > > Centro Nacional de Investigaciones Oncológicas (CNIO)
> > >
> > > (Spanish National Cancer Center)
> > >
> > > Melchor Fernández Almagro, 3
> > >
> > > 28029 Madrid (Spain)
> > >
> > > Fax: +-34-91-224-6972
> > >
> > > Phone: +-34-91-224-6900
> > >
> > > http://ligarto.org/rdiaz
> > >
> > > PGP KeyID: 0xE89B3462
> > >
> > > (http://ligarto.org/rdiaz/0xE89B3462.asc)
> > >
> > >
> > >
> > >
> > > **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y
> > > ...{{dropped:3}}
> > >
> > >
> > > _______________________________________________
> > >
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> > > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > >
> > > Search the archives:
> > > http://news.gmane.org/gmane.science.biology.informatics.conductor
> > >
> > >
> >
> >       [[alternative HTML version deleted]]
> >
> >
> >
>

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