Entering edit mode
Dear Mike, Wei, Adam, James,
I have to agree with Mike. If I understand it correctly, there is no
biological replication at all in this experiment. In that situation,
there is no way to assess statistical significance relative to
biological
variation.
limma has ways of making use of technical replicates, but there needs
to
be biological replication as well.
Best wishes
Gordon
> Date: Fri, 26 Mar 2010 09:49:13 +0100 (CET)
> From: Mike Walter <michael_walter at="" email.de="">
> To: bioconductor at stat.math.ethz.ch, Adam Kiezun <akiezun at="" gmail.com="">,
> Wei Shi <shi at="" wehi.edu.au="">
> Subject: Re: [BioC] Limma: technical replicates in multi-group
design
>
> 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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>
> -----Urspr?ngliche 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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