[BioC] Plot, plot and keep on plotting (follow-up to loess and limma)

[Naomi Altman]

Excuse me for ranting, but the need to do quality plots, actually 
look at the NUMBERS, not just p-values, etc cannot be 
over-emphasized.  And the less one understands the statistics, the 
more important it is to actually visualize your data.

--Naomi

At 11:39 AM 9/14/2006, john seers \(IFR\) wrote:

>Hi Wolfgang
>
> > so I am often also perplexed how people use such a
> >heavy gun without much thought.
>
>
>I am trying to avoid being one of those people. :)
>
>
>John
>
>---
>
>John Seers
>Institute of Food Research
>Norwich Research Park
>Colney
>Norwich
>NR4 7UA
>
>
>tel +44 (0)1603 251497
>fax +44 (0)1603 507723
>e-mail john.seers at bbsrc.ac.uk
>e-disclaimer at http://www.ifr.ac.uk/edisclaimer/
>
>Web sites:
>
>www.ifr.ac.uk
>www.foodandhealthnetwork.com
>
>
>-----Original Message-----
>From: Wolfgang Huber [mailto:huber at ebi.ac.uk]
>Sent: 14 September 2006 15:58
>To: john seers (IFR)
>Cc: sdavis2 at mail.nih.gov; bioconductor at stat.math.ethz.ch
>Subject: Re: [BioC] loess and limma
>
>
>Hi John,
>
> > This worries me as people routinely slap in a loess normalisation.
>
>Non-parametric smoothing (such as loess) is an enormously powerful tool,
>but getting it right (especially at the boundaries) can be tricky, and
>there are parameters to choose such as the 'span' and the order of the
>local polynomials, so I am often also perplexed how people use such a
>heavy gun without much thought.
>
>There is some potential for over-fitting and smoothing out real signal.
>
>Well, that's my little rant for the afternoon :)
>
>  Best wishes
>  Wolfgang
>
>------------------------------------------------------------------
>Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111