[BioC] Bioconductor Digest, Vol 74, Issue 7

Christof Winter winter at biotec.tu-dresden.de
Thu Apr 9 15:06:16 CEST 2009

vasantika s wrote, On 09.04.2009 12:10:
> Hi,
> I have a scatterplot of 2 chips against each other. Now my problem is ..
> I have a list of affyids, which I want to plot in a different colour(say
> red) on this scatterplot. How do I go about doing this?
> I searched the list archives, but got nothing! Sorry, if it is a too
> simplistic question.
> thanks,
> V

Hi V,

assuming that eset is an ExpressionSet object and affy.ids a vector of 
Affy probesets, this will do it:

 > plot(exprs(eset[, 1]), exprs(eset[, 2]))
 > points(exprs(eset[affy.ids, 1]), exprs(eset[affy.ids, 2]), col="red")

You might want to change 1 and 2 to some of your sample names.


Christof Winter
Bioinformatics Group
Biotechnologisches Zentrum
Technische Universität Dresden
Tatzberg 47-51
01307 Dresden

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