[BioC] unwrapdups for duplicate spots on custom array

Steffen Neumann sneumann at ipb-halle.de
Wed Mar 8 15:36:55 CET 2006

[This is a repost of a message sent 20hrs ago, which didn't appear
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I am currently working on the analysis of the SGED Study 073,
which has been performed with the potato_10K_v3_sep14_2004 chip,

I found that the pattern for replicated spots is non-trivial,
duplicates are within a block, but with the upper-left spots 
duplicated in the lower right of a block, and lower left spots
replicated on the upper right. 

The spacing is 220 for spots in the rectangle (1,1) through (13,18) 
and 455 for spots in (14,1) to (26,8). A plot of the pairs
is available at msbi.ipb-halle.de/~sneumann/lines.pdf

I'd like to use calculate the duplicateCorrelation and do an lmFit.

Should I 
       1) hack unwrapdups to understand this/any layout
       2) hack/rearrange the inputfiles, possibly with side-effects
          for the normalization (?!)
       3) Do something completely different ?

Checking the Archive I found very few references to duplicates 
which are not "columns" , "rows" or "topbottom". Did I miss something ?


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