[BioC] duplicate correlation of 4 "within array replicates" limmaGUI

Philipp Pagel p.pagel at wzw.tum.de
Tue Oct 14 14:07:33 CEST 2008

> I attached a schema of the slide-design, also with an example of the 4
> replicates, hoping that like this I could explain it sufficiently.
> For my understanding the replicates are regularly arranged.

Yes, the replicates on these Exiqon arrays are spaced evenly and at some
point I did compute the actual spacing. As you already mentined there
are 4 identical sets and the resulting spacing is the number of genes in
each of them.

Then I discovered that it is a lot more conveniant to simply sort the
data by ID - that way you have exactly one requirement: Each spot needs
to be replicated the same number of times, while the exact layout,
number of genes, blocks etc. becomes irrelavant:

	MA2 = MA[order(MA$genes$ID), ]
	dupfit = duplicateCorrelation(MA2, ndups=4, spacing=1)
	fit <- lmFit(MA2, ndups=4, spacing=1, correlation=dupfit$consensus, design=MA2$design)
	fit <- eBayes(fit)


Dr. Philipp Pagel
Lehrstuhl für Genomorientierte Bioinformatik
Technische Universität München
Wissenschaftszentrum Weihenstephan
85350 Freising, Germany

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