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

[john herbert]

Thank you Clause,
Yes, I would say this is evident in my data as I have very red-up
genes and very green-down genes but not much in-between. I could use
scatterplot3d but if you have any other suggestions, much appreciated.
Thank you.

John.

On Mon, Nov 14, 2011 at 2:21 PM, Mayer, Claus-Dieter <c.mayer at abdn.ac.uk> wrote:
> Hello,
>
> One issue I found with using the single channels of a two-colour experiment in a multivariate visualisation technique (PCA plots, clustering, heatmap, etc) is that array or dye effects can mask the sources of variation you are mostly interested in. Strong array effects mean that the two channels from the same array cluster together, strong dye effects can result in the red and green channels forming two big groups (normalisation can only eliminate these effects to a certain extent).
> In a PCA (or similar ordination method) it thus often makes sense to look at higher components (not only the first two).
>
> Best Wishes
>
> Claus
>
> Dr. Claus-D. Mayer
> Biomathematics & Statistics Scotland (BioSS)
> Rowett Institute of Nutrition and Health
> University of Aberdeen
> Aberdeen AB21 9SB, Scotland, UK.
> email: claus at bioss.ac.uk or c.mayer at abdn.ac.uk
> Telephone: +44 (0) 1224 716652
>
> Biomathematics and Statistics Scotland (BioSS) is formally part of The James Hutton Institute,
> a  registered Scottish charity No. SC041796 and a company limited by guarantee No. SC374831
>
>
>> -----Original Message-----
>> From: bioconductor-bounces at r-project.org [mailto:bioconductor-
>> bounces at r-project.org] On Behalf Of mjonczyk
>> Sent: 14 November 2011 10:52
>> To: arraystruggles at gmail.com; bioconductor at r-project.org
>> Subject: Re: [BioC] Two channel data vs. one colour data for PCA,
>> heatmaps and clustering
>>
>> 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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>
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>