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

[Naomi Altman]

Thanks.  And of course I meant to take log(pm(Affydata),2)) - 
otherwise it is hard to see the low expression values.

--Naomi

At 02:47 PM 2/23/2006, Wolfgang Huber wrote:
>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
>
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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)
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