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

[mjonczyk]

Dear John,

I suppose that for the two-colour experiment you have also "A" (average 
expression) values.
I don't know what package you have used but limma has RG.MA function
which transforms MA data to RG (i.e. unlogged intensities).
So you could construct MAlist object from your data, transform it to 
RGlist,
(maybe take a log2) and you will have data for both channels.

HTH,
Maciej Jończyk

> 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.

-- 
Maciej Jonczyk,
Department of Plant Molecular Ecophysiology
Faculty of Biology, University of Warsaw
02-096 Warsaw, Miecznikowa 1
Poland



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