[BioC] Limma: technical replicates in multi-group design

[Adam Kiezun]

Dear Wei,
Thank you for your response. The design you propose is in fact exactly
what I use right now. I agree with Michael though - I think I need to
explicitly indicate to limma that my replicates are technical. In the
manual, the duplicateCorrelation function is used for this purpose in
a two-channel array. My question is then how to use
duplicateCorrelation in a single-channel analysis.

./adam

On Thu, Mar 25, 2010 at 6:37 PM, Wei Shi <shi at wehi.edu.au> wrote:
> Dear Adam:
>
>   You can use the following commands to create a design matrix for your
> experiment:
>
> s <- factor(c("A","A","B","B","C","C"))
> design <- model.matrix(~0+s)
> colnames(design) <- levels(s)
> fit <- lmFit(x,design)
>
>   To do a pairwise comparison, you can use the makeConstrasts function:
>
> contr <- makeContrasts(A-B,A-C,B-C,levels=design)
> fit.contr <- eBayes(contrasts.fit(fit,contr))
>
> Cheers,
> Wei
>
> Adam Kiezun wrote:
>>
>> Hi,
>> How do I write the design matrix to specify technical replicates in
>> multi-group experiment on a single-channel array (data coming from
>> lumi)?
>>
>> I have 3 groups of samples (A, B, C), each group has 2 technical
>> replicates (so I have 6 expression vectors: A1, A2, B1, B2, B3). How
>> do I write the design matrix to tell limma that A1 and A2 etc are
>> technical replicates and that I want to do all pairwise comparisons
>> between groups (ie. AvsB, AvsC, BvsC)?
>>
>> The limma manual covers technical replicates for two-channel arrays,
>> and the multi-group experiments with biological replicates. I'd like
>> to know how to deal with a one-channel arrays, multi-group experiment
>> with technical replicates.
>>
>> regards
>> Adam
>>
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>
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