[BioC] unwrapdups for duplicate spots on custom array
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
on the list -- apologies if you received this twice.]
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.
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 ?
More information about the Bioconductor