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

[Mike Walter]

Dear Wei,

In my opinion the way you construct the design matrix the technical replicates are treated as independent samples. The technical replicates are handled with the block argument in the duplicateCorrelation() function. As I understand the experimental design, however, there are only technical but no biological replicates. I have data from the same type of experiment and told the guys that there is no way of using any statistical method to analyse their data. Am I right or is it possible to use limma in such a case?

Kind regards,

Mike
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-----Ursprüngliche Nachricht-----
Von: Wei Shi 
Gesendet: 25.03.2010 23:37:26
An: Adam Kiezun [
Betreff: Re: [BioC] Limma: technical replicates in multi-group design

>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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