[BioC] plate vs. pin-tip

[Wolfgang Huber]

Hi Johanna,

print-tip and plate are usually "orthogonal" factors, in the following 
sense: print-tip corresponds to spatial sectors on the array, whereas 
plate corresponds to the 384- or 96-well plates in which the DNA was PCR 
amplified, stored, and brought to the spotter. Often you can visually 
identify plate effects as gradients or particularly bright or dark rows 
within a sector. Whether the plate effects are technical noise that 
needs to be normalized away, or whether they are true biological signal 
depends very much on the experiment - often, different plates correspond 
to different clone libraries e.g. from different tissues.

marray (and may I note vsn as well) currently allow only estimation of 
either print-tip or plate effects. But one could imagine a (generalized) 
linear model that fits both, just nobody seems to have implemented this 
yet - or has anyone?

   Best wishes
    Wolfgang

Johanna Hardin wrote:
> We're using marrayNorm to normalize our data, and we'd like to normalize
> with respect to pin-tips as well as arrays.  However, our choices
> include plate normalization.  Can someone describe the difference
> between pin-tip and plate normalization (is it possible that we only
> have pin-tip issues and not plate issues?)
> 
>  
> 
> Additionally, does marrayNorm have a global normalization?  And is
> global normalization synonymous with array normalization?
> 
>  
> 
> Thanks, Jo
> 
>  
> 
> Jo Hardin
> 
> Assistant Professor
> 
> Department of Mathematics
> 
> Pomona College
> 
> 610 N. College Ave.
> 
> Claremont, CA 91711
> 
> 909-607-8717
> 
> jo.hardin at pomona.edu
> 
>  
> 
> 
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> 
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-- 
Best regards
   Wolfgang

-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber