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

[James W. MacDonald]

Hi Adam,

Adam Kiezun wrote:
> 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.

This is outlined in both the Limma User's Guide, and the help page for 
duplicateCorrelation().

 From ?duplicateCorrelation:

Details:

      When 'block=NULL', this function estimates the correlation between
      duplicate spots (regularly spaced within-array replicate spots).
      If 'block' is not null, this function estimates the correlation
      between repeated observations on the blocking variable. Typically
      the blocks are biological replicates and the repeated observations
      are technical replicates.

so

dupcor <- duplicateCorrelation(x, design, block=rep(1:3, each = 2))

should be what you want.

Best,

Jim


> 
> ./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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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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