Thanks Vincent and James

As James pointed it is the output of two for loop
but for every 10 fold validation it prints ((30+6) X 10 )) ~ 360 character
which is of no use and takes some time,
if we can save that time lets approx 10 sec in each runs than on 1000
simulations everybody can save atleast 2.7 hrs.

The similar way as suggested by Vincent ,I modified the code
pamr.listgenes.r to stop printing the genelist after extracting the gene
list . In case of small subset of genes it doesn't matter
but it takes time to print in case of larger set of genes (more than 10K),

I tried to find nsccv.R, in my linux machine but it is not there,
I found the script pamr which has the structure for fold printing , but
could not get success.


On Fri, Feb 27, 2009 at 5:16 PM, James MacDonald <jmacdon@med.umich.edu>wrote:

> Hi ALok,
>
> I think you are mistaken. It is very unlikely that it would take R 60
> seconds to print a number to stdout. Instead, what is happening is the
> printing of the numbers is from a for() loop (that is within another for()
> loop) that also runs the crossvalidation. So what takes the 60 seconds is
> the fitting of the pam model, not the printing of the fold index.
>
> The authors have hard-coded this printing into their code, so unless you
> want to make modifications, you won't be able to stop it.
>
> Best,
>
> Jim
>
>
>
> James W. MacDonald, M.S.
> Biostatistician
> Hildebrandt Lab
> 8220D MSRB III
> 1150 W. Medical Center Drive
> Ann Arbor MI 48109-0646
> 734-936-8662
> >>> ALok <foralok@gmail.com> 02/26/09 4:04 PM >>>
> Hi All
>
> I am using  pamr.cv to cross validate the NSC classifier,
> function runs smoothly with no error,
> but unnecessarily it is printing each Fold index as
>
> Fold 1 :123456789101112131415161718192021222324252627282930
> Fold 2 :123456789101112131415161718192021222324252627282930
>
> which takes approx *60 sec* for each *10 fold CV *runs with *4GB* memory
> while runnning 10K simulations this factor will increase 10K times
> i.e approx *1.6 hrs *
>
> i have to do *10,000* iteration for each 10 fold CV for several datasets
> and in each run it takes more than *15 hrs* just to print the Fold index ,
> which is not needed by  any user in any case .
>
> My question is that
> Is there any way to stop printing Fold index on screen , so that simulation
> time can be reduced
>
>
> Thanks in advance
>
> Regards
> ALok
>
> --
> Ph.D scholar
> Centre of Computational Biology and Bioinformatics
> School of Information Technology
> JNU New Delhi
>
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-- 
Ph.D scholar
Centre of Computational Biology and Bioinformatics
School of Information Technology
JNU New Delhi

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