[BioC] LIMMA - within and between array technical replicates

[Dries Knapen]

Hi,

In lmFit(object, correlation), "correlation" is "the inter-duplicate  
_or_ inter-technical replicate correlation".

Correlation is calculated using duplicateCorrelation(object, ndups,  
block), where "ndups" is the number of spot replicates, and "block"  
is used to describe technical replicates.

The help entry for duplicateCorrelation() says that "At this time it  
is not possible to estimate correlations between duplicate spots and  
between technical replicates simultaneously. If block is not null,  
then the function will set ndups=1."

So what would be the best way to deal with both duplicate spots _and_  
technical replicates of arrays? Calculate both, and use the most  
conservative (which is what duplicateCorrelation() implicitly does by  
assuming that between-array correlations are lower than within-array  
correlations I guess)? Calculate both, and use some kind of weighed  
average? Does someone have experience with this issue?

thanks,
Dries Knapen




********************************************
Dr. Dries Knapen

University of Antwerp
Department of Biology
Ecophysiology, Biochemistry and Toxicology
Groenenborgerlaan 171 - U711, B-2020 Antwerp
Belgium

tel ++32 3 265 33 49
fax ++32 3 265 34 97