[BioC] Spotted array analysis

[Ron Ophir]

Dear group members,
I working with marrayXXX packages on genepix file. I wonder which channel is used as a reference, Green or Red, when the maNorm() function generates the "maM" matrix. Does M is log(R/G) or vise versa. I'm asking that because I analyze a dye swap experiment and I realize that I have to swap my self the reference for further analysis. I there a dye swap normalization function that does it automatically?
Thanks in advance,
Ron

Ron Ophir, Ph.D.
Bioinformatician,
Biological Services
Weizmann Institute of Science
POB 26
Rehovot 76100
Israel
e-mail: Ron.Ophir at weizmann.ac.il
Phone: 972-8-9342614
Fax:972-8-9344113