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>:

> 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>:
>>
>>
>>> On Fri, Feb 21, 2014 at 11:25 AM, Giovanni Calice <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
>

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