[BioC] MAANOVA - how to collapse replicate spots

[Cecilia McGregor]

Hi

I am using maanova and have duplicate spots on my array. I want to collapse these duplicates after rlowess transformation. In the April 25 2008 Manual they describe how to do it with 'createData' but that does not seem to be an option anymore. It is not mentioned in the January 23 2008 manual and doesn't work when I try it. I know I can add Spot as a random variable to the model, but it does make computation time significantly longer. I also know that I can manually take the average of the spots before inputting the data into maanova, but if possible I would rather first do the 'rlowess' transformation before collapsing.

Just for your info my experiment has: 2 cultivars, 2 treatments, 4 timepoints, 4 biological reps, 2 spots per EST on array.

I'm pretty inexperienced with R, so I hope this is not too stupid a question. Any ideas?

Thanks

Cecilia


Cecilia McGregor, Ph.D.
Sweetpotato Breeding and Genetics Lab
School of Plant, Environmental and Soil Sciences
236 J.C. Miller Hall
Louisiana State University
Baton Rouge
LA, 70803
USA

Phone: (225) 763-9138
Fax: (225) 578-1068