[BioC] bumphunter DMRs difficulties
James W. MacDonald
jmacdon at uw.edu
Mon Feb 24 15:37:20 CET 2014
Hi Giovanni,
Tim advised you to do the exact opposite. If you set B = 100, then the
smallest p-value you can achieve is 0.01, which as he says, 'sucks'. If
you use B = 1000, the smallest p-value will be 0.001 which is marginally
better.
Best,
Jim
On 2/24/2014 5:46 AM, Giovanni Calice wrote:
> Hi Tim,
> I'm already in the order of ideas to set the n of resamples below
> about 100 as you say.
> I await news about your comments for a better marginal test statistic and
> the reference discussion about this topic.
>
> For now I'll follow your advice and previous ones.
>
> Thank you very much.
>
> Best,
> Giovanni
>
>
> Laboratory of Preclinical and Translational Research
> IRCCS - CROB Oncology Referral Center of Basilicata
> Rionero in Vulture - Basilicata - Italy
>
>
> 2014-02-23 5:47 GMT+01:00 Tim Triche, Jr. <tim.triche at gmail.com
> <mailto:tim.triche at gmail.com>>:
>
> Don't do that. B is the number of permutations. Your
> significance estimates will suck if you set it below about 100.
> If you can wait (a day or so) for 1000 or more permutations, they
> will be quite good. I have some ideas for a better marginal test
> statistic to capture the omnibus null of "no difference" against
> any reasonable alternative, but that's a topic for another
> discussion. It won't change the fact that you need a lot of
> permutations to get solid significance estimates from a biased
> sample (450k chip).
>
> Best,
>
>
> Statistics is the grammar of science.
> Karl Pearson <http://en.wikipedia.org/wiki/The_Grammar_of_Science>
>
>
> On Sat, Feb 22, 2014 at 10:02 AM, Giovanni Calice
> <giovcalice at gmail.com <mailto:giovcalice at gmail.com>> wrote:
>
> Hi,
>
> I missed to ask advice about B parameter.
> In my first bumphunter runs, I set B=1 (default setting)
> having thus
> results within a reasonable time.
>
> Now, as mentioned in the previous mail, I set B=1000 according
> to the reference
> manual and
> I thought so in order to have a statistically significant results.
>
> In my next bumphunter call, have I to change this setting
> (B=1000)?
>
> Thanks,
> Giovanni
>
>
> Laboratory of Preclinical and Translational Research
> IRCCS - CROB Oncology Referral Center of Basilicata
> Rionero in Vulture - Basilicata - Italy
>
>
> 2014-02-21 18:53 GMT+01:00 Giovanni Calice
> <giovcalice at gmail.com <mailto:giovcalice at gmail.com>>:
>
> > 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 at uw.edu <mailto:jmacdon at 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 <http://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 at uw.edu <mailto:jmacdon at uw.edu> <mailto:
> >>> jmacdon at uw.edu <mailto:jmacdon at 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 at jhsph.edu <mailto:khansen at jhsph.edu>
> <mailto:khansen at jhsph.edu <mailto:khansen at jhsph.edu>>>:
> >>>
> >>>
> >>>
> >>> On Fri, Feb 21, 2014 at 11:25 AM, Giovanni Calice
> >>> <giovcalice at gmail.com
> <mailto:giovcalice at gmail.com> <mailto:giovcalice at gmail.com
> <mailto:giovcalice at gmail.com>>>wrote:
> >>>
> >>>
> >>> 273952
> >>>
> >>>
> >>>
> >>> This is a crazy number of putative bumps
> >>>
> >>> Kasper
> >>>
> >>>
> >>> [[alternative HTML version deleted]]
> >>>
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> >>> conductor
> >>>
> >>>
> >>> --
> >>> 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
> >>
> >>
> >
>
> [[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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