[BioC] Fw: random location of duplicate spots and use of limma

[Ingunn Berget]

Hello

There are approximately 6000 different genes on the arrays, there are two spots for each gene
The duplicated spots have random location, which means that the number of spots between each duplicate is not the same for every gene. This is the summary for the distances:

  Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   4.00   32.00   71.00   86.59  135.00  244.00 

(Distance here means number of spots between the two duplicates)

The function duplicateCorrelation in limma can be used to estimate correlation between within-array duplicates, the methodology is based on the assumption that duplicates are equally spaced. Since this assumption is not fulfilled here does this means that I cannot calculate the correlations and must take the average of the duplicates? Are there some functions to do this in limma or other BioC packages?


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Ingunn Berget
Norwegian University of Life Sciences
Department of Animal and Aquaculture


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