[BioC] LIMMA: Duplicate spots

Philipp Pagel p.pagel at wzw.tum.de
Wed Jul 23 22:39:07 CEST 2008

> I haven't used LIMMA for a while, but I remember that when I did there
> was a special way to handle duplicate spots. However the layout of the
> array had to be such that one replicate was printed first for all
> spots and then the other replicate, because somewhere you had to say
> something like there are 5000 spots and the next rep starts at spot
> number 5001.

You are referring to something like this:

dupfit <- duplicateCorrelation(MA, ndups=2, spacing=5000)
fit <- lmFit(MA, ndups=2, spacing=5000, correlation=dupfit$consensus)

> The reason I'm asking is because I'm developing Agilent arrays and
> they randomize everything so it would not be possible to say the
> duplicate spots start at a specific place.

As long as there is exactly the same number of replicate spots for each
probe you could reorder the data beforehand to get consecutive replicate
spots - e.g. by Gene ID:

MA <- MA[order(MA$genes$ID), ]
dupfit <- duplicateCorrelation(MA, ndups=2, spacing=1)
fit <- lmFit(MA, ndups=2, spacing=1, correlation=dupfit$consensus)


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

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