[BioC] bumphunter DMRs difficulties

[James W. MacDonald]

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 at jhsph.edu>:
>
>>
>> On Fri, Feb 21, 2014 at 11:25 AM, Giovanni Calice <giovcalice at 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
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Seattle WA 98105-6099