Dear Bioconducters, 
 
I found a lot of information about dye-swap effect and its control here (Thanks a lot). With this information, and using Limma, I know I have dye-swap effect in some of my genes (more than 200), and I know also I can use Limma to control this effect, but I want to use RankProduct. 
 
Once I have my data normalized, I apply RP, and I found some of dye-swap affected genes in the output list of RP, because I did nothing to control the dye-swap. My question is then, if Is there any way to "remove" or consider the dye-swap effect using RP? or Is there any way to correct it before use RP? 
 
Some data: I'm working with C. elegans, two-color microarray (18) and three treatments with the following design:
 
SlideNumber    Cy3    Cy5
1       Control         Treatment3
2       Control         Treatment1
3       Control         Treatment1
4       Treatment1   Control
5       Treatment1   Control
6       Control         Treatment3
7       Control         Treatment1
8       Treatment3   Control
9       Treatment3   Control
10      Control        Treatment3
11      Treatment3  Control
12      Treatment1  Control
13      Control        Treatment2
14      Control        Treatment2
15      Control        Treatment2
16      Treatment2  Control
17      Treatment2  Control
18      Treatment2  Control
 
Thanks a lot any clue, 
 
Ana. 
 
 
--------------------------------------------------
Ana Viñuela Rodriguez
PhD student.
Laboratory of Nematology
Wageningen University
Binnenhaven 5
6709 PD, Wageningen
The Netherlands
Tel: +31 317 483444/482197
Fax: +31 317 484254 


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