After normalization, which could rely on the chip layout, you can order your data by gene, and assume a spacing of 1
i.e.
MA<-MA[order(RG$genes[,"Name"]),]
corfit <- duplicateCorrelation(MA, ndups=4, spacing=1)

this assumes that:
- there is a  Name column in the gens slot that contains the same value for each replicate spot
- each gene is replicated exactly 4 times
- if multiple probes are used for a gene they have different names

-----Original Message-----
From: bioconductor-bounces@stat.math.ethz.ch on behalf of Hua Weng
Sent: Mon 23-Jan-06 9:22 PM
To: 'Gordon Smyth'; 'BioC Mailing List'
Subject: Re: [BioC] limma: irregular spacing between within-array replicates
 
Hi, Dr. Smyth and Bioconductor mailing list:

 

Dr. Smyth, Thank you very much for making such a nice package, limma, for
microarray analysis. 

 

I have a question for irregular spacing for within-array replicates. I have
four technical replicates on one array, but the spacing between them is not
regular. The spacing between the first and second replicates is 16, the
spacing between the second and third is 176, and the spacing between the
third and the fourth is 16 again. How can I calculate correlation for within
array replicates based on irregular spacing to make full use of within array
replicates?

 

I highly appreciate any suggestions and comments.

 

Hua Weng

Microarray Core Facility

Oklahoma State University 


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