[BioC] Log intensity plots with colours

[Georg Summer]

library(lattice)

xyplot(fc ~ grp1,data=toplot,groups=res,xlab="Log2
Intensity",ylab="Log2 Fold
Change",auto.key=list(text=c("down","not","up")))

toplot contains the intensity (e.g grp1) and foldchange (as e.g.
obtained by limma's topTable) and res is the result as obtained by
limma's decideTests for the contrast you use.

toplot:
grp1 grp2 fc res


Georg

On 31 May 2011 16:13, john herbert <arraystruggles at gmail.com> wrote:
>  Dear Bioconductors,
> I would like to generate a scatter plot of single colour array data where;
>
> 1) up-regulated genes with FDR <= 0.05, points are coloured in red
> 2) down-regulated genes with FDR <= 0.05, points are coloured in blue
> 3) all other points are in green/other colour
>
> I know I can do volcano straight from Limma but a simple scatter plot with
> colours would be useful.
>
> Thanks.
>
>        [[alternative HTML version deleted]]
>
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