Hi Jim,

Ok!
My next bumphunter call will be on 1/3 of total ncores (I share compute
cycles with co-workers too)
with cutoff and cutoffQ = 0.95.

Many Thanks.

Best,
Giovanni

Laboratory of Preclinical and Translational Research
IRCCS - CROB Oncology Referral Center of Basilicata
Rionero in Vulture - Basilicata - Italy



2014-02-21 18:29 GMT+01:00 James W. MacDonald <jmacdon@uw.edu>:

> Hi Giovanni,
>
> I don't know about the number of cores. I share compute cycles with
> co-workers, so can't just hog them all up. A recent bumphunter run I did on
> our shared server (a single multi-core machine with I believe 32
> processors) was:
>
> library(doParallel)
> registerDoParallel(cores = 12)
> bmps.main <- bumphunter(eset, design.cd, cutoff = 0.99)
>
> Which resulted in something like 2500 bumps and finished in, I don't know,
> say 15-20 minutes?
>
> Best,
>
> Jim
>
>
>
> On 2/21/2014 12:21 PM, Giovanni Calice wrote:
>
>> Hi Jim,
>>
>> the call for bumphunter is:
>>
>> bumphunter(myGenomicRatioSet, design=designMatrix, cutoff=0.05, B=1000,
>> verbose=TRUE)
>>
>> I set cutoff to 0.05 not cutoffQ.
>> Next bumphunter call I will follow your advice;
>> regard to parallelize the process what is your suggestion?
>>
>> Would it be better to parallelize only on some of the ncores?
>>
>> Best,
>> Giovanni
>>
>> Laboratory of Preclinical and Translational Research
>> IRCCS - CROB Oncology Referral Center of Basilicata
>> Rionero in Vulture - Basilicata - Italy
>>
>>
>> 2014-02-21 17:52 GMT+01:00 James W. MacDonald <jmacdon@uw.edu <mailto:
>> jmacdon@uw.edu>>:
>>
>>
>>     Hi Giovanni,
>>
>>     You should give the actual call you used for bumphunter, rather
>>     than simply saying that you used 'recommended parameters'. It
>>     looks like you set cutoffQ to 0.05, which is exactly opposite to
>>     what you should be doing. Instead you should be using something
>>     like cutoffQ = 0.95.
>>
>>     Best,
>>
>>     Jim
>>
>>
>>
>>
>>     On Friday, February 21, 2014 11:36:32 AM, Giovanni Calice wrote:
>>
>>         Hi Kasper,
>>
>>         Thank you very much for the immediate response!
>>
>>           So,
>>           What do you suggest?
>>
>>         Giovanni
>>
>>         Laboratory of Preclinical and Translational Research
>>         IRCCS - CROB Oncology Referral Center of Basilicata
>>         Rionero in Vulture - Basilicata - Italy
>>
>>
>>         2014-02-21 17:27 GMT+01:00 Kasper Daniel Hansen
>>         <khansen@jhsph.edu <mailto:khansen@jhsph.edu>>:
>>
>>
>>
>>             On Fri, Feb 21, 2014 at 11:25 AM, Giovanni Calice
>>             <giovcalice@gmail.com <mailto:giovcalice@gmail.com>>wrote:
>>
>>
>>                 273952
>>
>>
>>
>>             This is a crazy number of putative bumps
>>
>>             Kasper
>>
>>
>>                 [[alternative HTML version deleted]]
>>
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>>
>>     --
>>     James W. MacDonald, M.S.
>>     Biostatistician
>>     University of Washington
>>     Environmental and Occupational Health Sciences
>>     4225 Roosevelt Way NE, # 100
>>     Seattle WA 98105-6099
>>
>>
>>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
>

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