My apologize for sending off topic to the list. I, with the help of the user's guide and of the html_help, I set up the following contrast matrix: > design time1 time2 time3 1 1 0 0 2 1 0 0 3 1 0 0 4 0 1 0 5 0 1 0 6 0 1 0 7 0 0 1 8 0 0 1 9 0 0 1 > contrast.matrix <- makeContrasts(time2-time1, time3-time2,time3-time1,levels=design) > contrast.matrix time2 - time1 time3 - time2 time3 - time1 time1 -1 0 -1 time2 1 -1 0 time3 0 1 1 Considering that my experiment relates levels of hidric stress, in other words, in the time zero there is no lack of water and, with the increase of the time, the shortage of water went increasing. Therefore, in the time x, larger than 3 (x>3), the plants died for lack of water. I can generate 3 tables of genes, one for the contrast 1, one for the 2 and one for the contrast 3. My doubt is the following: can I say that the genes of the table 1 are the genes differentialy expressed in the time 1? Can I say that the genes of the table 3 are the genes differentialy expressed in the time 2? same for the time 3? Maybe I don't know how to formulate a question in English that really characterizes my doubt, therefore, if somebody can explain to me, shortly, an interpretation for this contrast matrix, would be very welcome. Thanks very much -- Marcelo Luiz de Laia, M.Sc. Dep. de Tecnologia, Lab. Bioqu?mica e de Biologia Molecular Universidade Estadual Paulista - UNESP Via de Acesso Prof. Paulo Donato Castelane, Km 05 14.884-900 - Jaboticabal, SP, Brazil PhoneFax: 16 3209-2675/2676/2677 R. 202/208/203 (trab.) HomePhone: 16 3203 2328 - www.lbm.fcav.unesp.br - mlaia@yahoo.com

On 1/29/04 2:16 PM, "Marcelo Luiz de Laia" <mlaia@fcav.unesp.br> wrote: > My apologize for sending off topic to the list. > > I, with the help of the user's guide and of the html_help, I set up the > following contrast matrix: > >> design > time1 time2 time3 > 1 1 0 0 > 2 1 0 0 > 3 1 0 0 > 4 0 1 0 > 5 0 1 0 > 6 0 1 0 > 7 0 0 1 > 8 0 0 1 > 9 0 0 1 >> contrast.matrix <- makeContrasts(time2-time1, >> time3-time2,time3-time1,levels=design) >> contrast.matrix > time2 - time1 time3 - time2 time3 - time1 > time1 -1 0 -1 > time2 1 -1 0 > time3 0 1 1 > > Considering that my experiment relates levels of hidric stress, in other > words, in the time zero there is no lack of water and, with the increase of > the time, the shortage of water went increasing. Therefore, in the time x, > larger than 3 (x>3), the plants died for lack of water. > > I can generate 3 tables of genes, one for the contrast 1, one for the 2 and > one for the contrast 3. > > My doubt is the following: can I say that the genes of the table 1 are the > genes differentialy expressed in the time 1? Can I say that the genes of the > table 3 are the genes differentialy expressed in the time 2? same for the time > 3? Actually, as I understand what you are doing, the gene lists associated with the contrasts would represent the genes differentially expressed between time 1 and time 2, time 2 and time 3, and time 1 and time 3. Are these two-color arrays? If so, then the gene lists you find by fitting your data with the design matrix will give you the genes differentially expressed between your "treated" group and your control group. In other words, the first column would represent genes differentially expressed at time 1 (compared to the control), the second at time 2, and the third at time 3. If they are not two-color arrays, then you probably want to decide on a reference (perhaps the "no-lack-of-water" state at time 1 and your contrasts would be between time 2 and time 1 and time 3 and time 1. All of this depends, of course, on the biology and the hypotheses being tested. Sean -- Sean Davis, M.D., Ph.D. Clinical Fellow National Institutes of Health National Cancer Institute National Human Genome Research Institute Clinical Fellow, Johns Hopkins Department of Pediatric Oncology --