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Dear Seungmin, You are at a university with one of the top departments of Statistics and Biostatistics. Probably there is a Statistical Consulting Center. Even if the SCC consultants do not know limma or Bioconductor, they can help set up the model and the contrasts. (Of course, Berkeley is the Ph.D or professional home of many Bioconductor contributors.) However, if all you want is to select genes that differentially express under at least one condition, you could use 1-way ANOVA, using the treatment names you have displayed below. I do not have the manual in front of me, but I am sure it is one of the examples. You do not need to fit this as a factorial experiment. You can use the ANOVA F-test as recently discussed on this forum, or you can use the individual t-tests. --Naomi Altman At 01:29 PM 11/9/2006, lee wrote: >Hello, > > I have mouse 8 hybridization Groups. > 2 tissues (Ent, Liv) > 2 ages (4wk, 8wk) > 2 different diets. (IOL,ID) compared to control diet > 2 different mutation.(sla, HFE) compared to wild type. > > The following is the names for each hybridization group. > "sla4wkEnt","HFE4wkEnt", > "HFE4wkLiv","sla4wkLiv","IOL4wkLiv", > "HFE8wkLiv","ID8wkLiv","IOL8wkLiv" > > I have at least 4 hybridizations for each hybridization group. > Most of them have around 6 ~12 hybridizations. > > Each hybridization represents individual biological samples(mouse). > I have switched dyes to label control or experimental samples. > For example, 3 of experimental mouse samples were labeled with > Cy5 and 3 of them are labeled with Cy3. > > I studied LIMMA program and was able to read all gpr files and > normalize the data. > After this, I don't know how to design and make contrast to know > which genes are significantly different at least one group among 8 > hybridization groups. > > After finding out the candidate genes, I want do cluster analysis > to find out which hybridization groups are similar in terms of gene > expression profiling and which gene groups behave similarly across > different hybridization groups. > > I studied User's Guide a lot. But most of them are for Affy data. > After trying copying and modifying examples on my own, I find out > it is out of my ability to do analysis for my data. Could you help > me how to do this kind of analysis or give me detailed examples > that I can use with modification for my data? > > Thank you so much for your help in advance. > > Seungmin > > > > >--------------------------------------------------------------------- -- >Seung-Min Lee > >graduate student >244 Morgan Hall >Molecular&Biochemical Nutrition >University of California at Berkeley >94720-3104 >lab phone (510)643-2351 >lab fax(510)642-0535 > > >--------------------------------- > > [[alternative HTML version deleted]] > >_______________________________________________ >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 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