Dear Cecilia, Please remember to cc the list even if you contact someone individually. Limma and MAANOVA can both handle loop designs and multi-way ANOVA. The way I do this is to use the single-channel normalization as in the Limma manual. For limma, I then proceed with the single-channel analysis as in the manual. "array" is the block. I am not that fond of setting up the contrasts for high order interactions, but it can be done. I have not used MAANOVA, so I am less than an expert. However, I would use the single-channel normalization and then use RG.MA to convert the normalized data back to normalized R and normalized G. Then I would proceed as if each channel were a normalized Affy array, except that there would be a random effect for array. I hope this helps. Naomi At 07:16 PM 6/17/2008, you wrote: >Dr Altman > >I was wondering whether you know of any microarray analysis program that >can handle loop designs, and three-term interactions? Maanova cannot do >what I need. Basically I have Cultivar, Time and Treatment. I've posted >many questions on the message boards but got no useful info. I've used >Limma before for other experiments with no problems, but I know that it is >not appropriate here. > >Any advise wold be much appreciated. > >Kind regards >Cecilia > >Cecilia McGregor, Ph.D. >Department of Entomology >404 Life Sciences Building >Louisiana State University >Baton Rouge >LA, 70803 >USA > >Office Phone: (225) 578-0518 >Lab Phone: (225) 578-0921 >Mobile Phone: (225) 763-9138 >Fax: (225) 578-1643 Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111