[GenABEL-dev] Precision and scientific notation in ProbABEL

[Yurii Aulchenko]

As a general rule I am for using scientific notation and 4 to 6 significant
digits (e.g. 0.123456E-20). This may be my FORTRAN background though :)

What if we decide to put say p-values in the outputs? Does the output
automatically switch to sci notation in this case?

YA


On Wed, Aug 14, 2013 at 12:03 PM, L.C. Karssen <lennart at karssen.org> wrote:

> Thanks for the input Nicola, I've set the output to 6 significant
> digits, although it seems that the cout function (used for printing)
> sometimes "eats" a trailing zero.
>
>
> Best,
>
> Lennart.
>
>
> On 30-07-13 10:33, Nicola Pirastu wrote:
> > Dear Lennart,
> >
> > I think that switching to scientific notation is not really necessary
> and could lead to a little of loss in precision unless of course you still
> > use 6 significant digits which will translate in just a reduction of 0
> in the values.
> > So if for example we were to choose scientific notation with 3
> significant digits, although this would not affect very much the final
> results we could be asked to submit more and
> > would not be able to comply.
> > So to summarize I think that if it does not have any effect on
> performance of ProbABEL 6 significant digits without scientific notation is
> fine.
> >
> > Best
> >
> > Nicola
> >
> >
> > Dr. Nicola Pirastu PhD
> > Research Fellow
> > Medical Sciences, Chirurgical and Health Department
> > University of Trieste
> > Medical Genetics
> > IRCCS Burlo Garofolo
> > Via dell'Istria 65/1
> > 34137 Italy
> > tel. +390403785539
> >
> > Il giorno 30/lug/2013, alle ore 09:32, "L.C. Karssen" <
> lennart at karssen.org> ha scritto:
> >
> >> Dear list,
> >>
> >> I'm finalising version 0.4.0 of ProbABEL and there are two things I'd
> >> like your opinion on:
> >>
> >> 1) with what precision should we print the betas, standard errors and
> >> Chi^2 values to the output files?
> >>
> >> 2) Should we use scientific notation in the output (for betas, standard
> >> errors and Chi^2)?
> >>
> >> In ProbABEL v0.3.0 and earlier output was simply sent to cout without
> >> any explicit formatting. In practice this lead usually to 6 significant
> >> digits, but sometimes less. My proposal is to fix the precision at 6
> >> significant digits.
> >>
> >> Regarding item 2): most of the betas I see are in the range between 0
> >> and 10, although in case of no effect beta's can be of the order of
> >> 1e-2, 1e-3. All in all, I don't think switching to scientific notation
> >> will improve the output.
> >>
> >>
> >> What are your opinions?
> >>
> >>
> >> Thanks,
> >>
> >> Lennart.
> >> --
> >> -----------------------------------------------------------------
> >> L.C. Karssen
> >> Utrecht
> >> The Netherlands
> >>
> >> lennart at karssen.org
> >> http://blog.karssen.org
> >>
> >> Stuur mij aub geen Word of Powerpoint bestanden!
> >> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> >> ------------------------------------------------------------------
> >>
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>
> --
> -----------------------------------------------------------------
> L.C. Karssen
> Utrecht
> The Netherlands
>
> lennart at karssen.org
> http://blog.karssen.org
>
> Stuur mij aub geen Word of Powerpoint bestanden!
> Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
> ------------------------------------------------------------------
>
>
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