[BioC] MAANOVA - how to collapse replicate spots

[Marcelo Laia]

Hi Cecilia,

Have you looked at the function  write.madata() after load maanova?
You could see a help about it on R by:

library(maanova)
?write.madata()

The "transform.madata()" function, if you had used it in your data
transformation procedure, returns an object of class 'madata'.

I hope this help

Marcelo

2008/4/25 Cecilia McGregor <cmcgre1 at lsu.edu>:
> 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
>
>  _______________________________________________
>  Bioconductor mailing list
>  Bioconductor at stat.math.ethz.ch
>  https://stat.ethz.ch/mailman/listinfo/bioconductor
>  Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>



-- 
Marcelo Luiz de Laia
Jaboticabal - SP - Brazil
sip:marcelolaia at ekiga.net

"Você vê as coisas como elas são e pergunta: por quê? Mas eu sonho com
coisas que nunca foram e pergunto: por que não? " - Bernard Shaw