Dear Wolfgang,

thanks a lot for your pointers to all the different packages.
To give you a bit more information about the experiment:

In this study, two factors are investigated: genotype and food.
Three different treatments were performed:

A) wt genotype + normal food
B) wt genotype + supplemented food
C) mutant genotype + supplemented food

Treatment/Genotype 	wt (W) 	mutant (M)
Normal food (N) 	x 	NA
Supplemented food (S) 	x 	x


(x = data available, NA = not available)

Each treatment was performed in four biological replicates, giving rise 
to 3 x 4 = 12 RNA samples.
These 12 samples were analyzed on four 3-color microarrays, 
competitively hybridizing one sample from each treatment (A,B,C) to one 
array.

Two contrasts are of interest to the researchers:

1.) For the wt genotype: genes with differential expression between the 
two food supplements (N, S)
2.) For "Supplemented food" (S) : genes with differential expression 
between wt and mutant genotypes (W, M)

As these two question each refer to a single factor (either genotype OR 
food), I could perform two separate analyses on the data e.g. by 
treating the arrays like standard two-color hybridizations and 
extracting only the two channels of interest each time.

Of course, I would be grateful for any advice,
thanks,

Thomas

Wolfgang Huber wrote:
> 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 
> arrays).
>
> To be more specific, I think you will need to reveal the biological 
> question and the experimental design behind these data.
>
>     Best wishes
>     Wolfgang
>
>
> [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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