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 > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor 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