[BioC] Two channel data vs. one colour data for PCA, heatmaps and clustering

[john herbert]

Dear Bioconductor.
In the past I have produced some PCA plots and heatmaps using one
colour data. On the PCA, it is useful to separate out the different
sample groups using the normalised expression values (say normal
coloured green and treatment coloured red).

However, this sort of analyses does not seem possible with two colour
as you have a sinlge log2 normalised ratio (M value) as input to PCA
and heatmap functions.

Does anyone have experience of doing PCA and/or heatmaps with 2 colour
data? Any info/advice appreciated.

John.