[BioC] Re: Limma: four suggestions related to weights and background correction

Ramon Diaz-Uriarte rdiaz at cnio.es
Thu Feb 26 16:19:47 MET 2004

> >However, regarding the type of normalization, I am not sure I see why, if
> >this
> >happens occasionally, the user should prefer global loess: if a print-tip
> >group in a specific array has been damaged (e.g., a scratch), but the rest
> > of the print-tip groups are OK, and the usual assumptions are believed to
> > hold for each of the other print-tip groups, then I think print-tip loess
> > is justified.
> Fair enough. My concern was that print-tip loess should only be used when
> there are a reasonable number of usable points in each print-tip group, say
> 100 or more. If you have no usable values in one group, then I worry that
> there might be only a small number of values in another group as well, yet
> enough that there would be no warning. In that case it would be much better
> to use "loess" or "robustspline".

Thanks for the comment. I understand the concern. At least in some of the 
cases we have seen, one or two print tip groups can be totally unusable, but 
the rest be fine (well in excess of 100 usable spots), as when an "accident" 
has taken place on one of the borders of the array. Anyway, I will more 
explicitly start looking for the possibility of some, though few, usable 
points, and let users know with a warning. 



> Best regards
> Gordon

Ramón Díaz-Uriarte
Bioinformatics Unit
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900

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