[GenABEL-dev] Precision and scientific notation in ProbABEL
L.C. Karssen
lennart at karssen.org
Sun Aug 18 23:20:38 CEST 2013
On 08/17/2013 10:38 AM, Yurii Aulchenko wrote:
> 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 :)
That seems too precise, given that most imput dosages/probabilities are
known to ~3 or 4 digits and I don't think that many phenotypes will be
measured more precisely.
>
> What if we decide to put say p-values in the outputs? Does the output
> automatically switch to sci notation in this case?
For p-values I would definitely go for scientific notation. We can turn
the on/off per output column (as each column is coded as a stringstream).
Lennart.
>
> YA
>
>
> On Wed, Aug 14, 2013 at 12:03 PM, L.C. Karssen <lennart at karssen.org
> <mailto: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 <mailto: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 <mailto: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 <mailto: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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> --
> -----------------------------------------------------
> Yurii S. Aulchenko
>
> [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter
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> <http://yurii-aulchenko.blogspot.nl/> ]
--
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
L.C. Karssen
Utrecht
The Netherlands
lennart at karssen.org
http://blog.karssen.org
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
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