[BioC] Duplicated spots in limmaGUI

[João Fadista]

Hi,

You can combine duplicate spots by ID with a script similar like this (assuming that your duplicated clones have a smaller ID than the ones that are not duplicated):

index <- order(MA$genes$ID)
MAsorted <- MA[index,]
MAsorted$printer$spacing <- 1

And then average the clones in the subset of the MAList where you have duplicated clones. Let say that your duplicated clones have an ID below 200000:

Subset <- MAsorted$genes$ID < 200000
MAsubset <- MA[Subset,]
 

If your clones that are duplicated have not a smaller ID than the ones that are not duplicated, you can make an extra column in your MAList where you can put a dummy ID where this is true.


Best regards

João Fadista
Ph.d. student


UNIVERSITY OF AARHUS
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E-mail:  Joao.Fadista at agrsci.dk
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-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Wonjong Moon
Sent: Thursday, April 19, 2007 2:46 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Duplicated spots in limmaGUI

Our slide design had some spots were duplicated and some were not. 
I am using limmaGUI, but duplicated spots were recognized by space between spots.
How can I handle the spots that were not duplicated? 
Should add flags in spottype file and exclude those? 

Is there any way to combine duplicated spots by ID or name in Limma? 

Thank you.

Wonjong.
Bioinformatician
SBRI.

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