[BioC] how to merge replicate spots?

[Naomi Altman]

When I use duplicateCorrelation, I get one contrast per gene, not per 
spot.  I am not sure what the problem is here.

The spots are aggregated in the fit, but of course any function such 
as plots that use the original data will not have this aggregation.

--Naomi

At 04:40 PM 7/3/2009, michael watson \(IAH-C\) wrote:
>If I were doing this, I would use the aggregate function to 
>calculate the mean for each of my genes, and then pass this averaged 
>data as a matrix to lmFit.
>
>There shouldn't be too many problems.
>
>Why don't you post your full code and any errors?
>
>________________________________
>
>From: bioconductor-bounces at stat.math.ethz.ch on behalf of Barbara Cegielska
>Sent: Fri 03/07/2009 8:13 AM
>To: bioconductor at stat.math.ethz.ch; r-help-bounces at r-project.org
>Subject: [BioC] how to merge replicate spots?
>
>
>
>Dear R-Users,
>
>I use home-made spotted arrays and every probe is printed in 
>triplicate. I normalized my data using limma package and I got mean 
>from these three replicates by using duplicateCorrelation function:
>
>
>design<-modelMatrix(targets, ref="HL60")
>duplicateCorrelation(MAl.pAq, design, ndups=3,spacing=1)
>corfit <- duplicateCorrelation(MAl.pAq, ndups=3, spacing=1, design)
>all.correlations <- tanh(corfit$atanh.correlations)
>fit <- lmFit(MAl.pAq, design, ndups=3, spacing=1, 
>correlation=corfit$consensus)
>contrast.matrix<-makeContrasts(AML.M2-K,levels=design)
>fit2<-contrasts.fit(fit,contrast.matrix)
>fit2<-eBayes(fit2)
>topTable(fit2,adjust="BH")
>
>However, this function does not change object dimmensions (plot 
>shows all spots, not only mean from all replicates), so I try to use 
>avedups function (a<-avedups(MA.normAq, ndups=3, spacing=1, 
>weights=NULL)), but I have problem with creating fit2, because of 
>differences in dimmentions. I would like to get a topTable object. 
>What shall I do??
>
>Regards,
>
>Barbara Cegielska
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111