[BioC] pairs plot - was: RNA degradation tends & options for analysis

[Wolfgang Huber]

Hi Naomi,


Naomi Altman wrote:
> One thing I find very useful is to look at
> 
> pairs(pm(myAffydata))
> 
 > [snip]
 >
> Incidentally, if some ambitious person would write a pairs routine 
> for hexbin, that would be both faster and more informative.

You can use the "smoothScatter" function in geneplotter (thanks to 
Florian Hahne) for this:

library("affydata")
library("geneplotter")
data("Dilution")

x = log2(pm(Dilution[, 1:3]))
pairs(x, panel=smoothScatter, add=TRUE)


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