[BioC] technical and biological replicates in the same Exprset - Agi4x44

[Gordon K Smyth]

Dear Paola,

I'm not sure why you say there's a problem.  duplicateCorrelation() has no 
difficulty with technical and biological replicates in the same 
experiment.

You might analysis your experiment by:

   targets$Treat <- factor(targets$Treat)
   design <- model.matrix(~Treat,data=targets)
   dupcor <- duplicateCorrelation(y,design,block=targets$Repl)
   fit <- lmFit(design,block=targets$Repl,correlation=dupcor$consensus)
   fit <- eBayes(fit)
   topTable(fit,coef=2)

Best wishes
Gordon

> Date: Tue, 8 May 2012 16:02:12 +0200
> From: Paola Sgado <sgado at science.unitn.it>
> To: bioc-devel at r-project.org
> Subject: [Bioc-devel] technical and biological replicates in the same Exprset - Agi4x44
>
> HI all,

> I'm having some problem with microarray analysis. I am a biologist not 
> very good with R neither with statistics!

> I'm using Agilent 4x44 arrays and the Agi4x44Processed package. I have 
> basically to compare WT vs KO data. The microarray was done first with 3 
> true biological replicates and later with 4 technical replicates with a 
> pool of RNAs.

> My design is the following:
>> targets
> FileName	Treat	GErep	Subject	Array Repl.
> 549_1_4.txt        KO     2	genotype     1   KO1
> 550_1_4.txt        KO     2	genotype     2   KO2
> 551_1_4.txt        KO     2	genotype     3   KO3
> 549_1_3.txt        WT     1	genotype     1   WT1
> 550_1_3.txt        WT     1	genotype     2   WT2
> 551_1_3.txt        WT     1	genotype     3   WT3
> 385_1_1.txt        WT     3	genotype     4   WT4
> 385_1_2.txt        KO     4	genotype     4   KO4
> 385_1_3.txt        WT     3	genotype     4   WT4
> 385_1_4.txt        KO     4	genotype     4   KO4
> 386_1_2.txt        WT     3	genotype     5   WT4
> 386_1_3.txt        KO     4	genotype     5   KO4
> 386_1_4.txt        WT     3 	genotype     5   WT4

> I performed normalization and filtering with the entire set of arrays, 
> but when I started the statistical analysis using ebayes with limma I 
> realized I could not treat biological (WT1,2,3-KO1,2,3) and technical 
> replicates (WT4-KO4) the same way.

> I tried to use the dupcor function, but it does not work with tech and 
> biol replicates in the same analysis. Is there a way to bypass the 
> problem?

> Thanks for your help, I really cannot find the way out....

> Cheers
> Paola


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