[BioC] Three-color microarray analysis

Wolfgang Huber whuber at embl.de
Sat Oct 16 02:01:38 CEST 2010

Hi Thomas

the NchannelSet class in the Biobase package can store such data [1], 
some of the normalisation [2] and QC-assessment [3] methods that are 
available for one- and two-color arrays can be either used directly or 
with a little adaptation to such data, as can the linear model based 
analysis of limma (e.g. by treating n 3-color arrays like 3n 1-color 

To be more specific, I think you will need to reveal the biological 
question and the experimental design behind these data.

	Best wishes

[1] Have a look at the vignette of the CCl4 package "From the Genepix 
data files to RGList to NChannelSet" for an example where such an object 
is constructed, which you will need to adapt to the particular file 
format your friend uses (you'll have to modify the read.images function 
or emulate it with calls to read.table).

[2] vsn, quantiles, ...

[3] boxplots, MA-plots, between-array distance heatmap, such as in the 
arrayQualityMetrics package

Il Oct/15/10 11:08 AM, Thomas Sandmann ha scritto:
> Dear all,
> I have received data obtained using a three-color microarray platform,
> e.g. three samples were labeled with three different fluorophores and
> hybridized competitively to a single array. Would anyone be able to
> point out a useful package for the analysis of three-color hybridizations ?
> Thanks a lot,
> Thomas

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