Re: [R] 'asymmetric span' for 2D loess?

From: Tokuyasu, Taku <Tokuyasu_at_cc.ucsf.edu>
Date: Tue, 03 Jun 2008 09:48:18 -0700

Dear Prof Ripley,

> > Hello,
> >
> > I am interested in performing a 2D loess smooth on microarray data, i.e.
> > log2 ratios on a 2D grid, using different spans in the horizontal and
> > vertical directions (the immediate reason being that replicate spots are
> > laid out in the horizontal direction). Is it possible to do this in R?
> > Functions like loess(stats) seem to apply the same span for all
> > predictors, which carries over to functions like ma2D(marray).
>
> See the next comment. 'span' applies to 2D distances, and I think you
> need to rescale your inputs so Euclidean distance is appropriate.

That's a great idea.

>
> > As an elementary second question, are there circumstances where one
> > expects to see a substantial difference in the fits between say loess(y
> > ~ x1 + x2) and loess(y ~ x1 * x2) with an interaction term (and if so,
> > what are they)?
>
> From the help page:
>
> formula: a formula specifying the numeric response and one to four
> numeric predictors (best specified via an interaction, but
> can also be specified additively). Will be coerced to a
> formula if necessary.
>
> So the two versions both specify smoothing in 2D.
>
> You can use things like lo(x1) + lo(x2) in some gam fits.

Hadn't thought of that, I will explore this.

>
> It often helps to read the primary sources, in this case chapters in the
> White Book (Chambers & Hastie, nominally 1992, actually published in
> 1991).
>
> --
> Brian D. Ripley, ripley_at_stats.ox.ac.uk
> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
> University of Oxford, Tel: +44 1865 272861 (self)
> 1 South Parks Road, +44 1865 272866 (PA)
> Oxford OX1 3TG, UK Fax: +44 1865 272595
>

Thanks very much for the help. Nice photos on the Web, by the way.

Regards,

_Taku

Taku A. Tokuyasu, PhD
UCSF Helen Diller Family Comprehensive Cancer Center San Francisco, CA 94143-0808



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