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

 	
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