I have microarray data to analyze with 3 factors: Genotype (wt, mut), Treatment (C, T), and Organ (s, r), each in 3 replicates. I found the guide for limma, I am just confused about how to "makeContrasts" to get all levels of main and interaction effect.

If this question is redundant, please provide the link, I could not find it.

Many thanks, Dan

Code should be placed in three backticks as shown below

# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )

https://f1000research.com/articles/9-1444/v1 may answer your questions.

As we try to explain in the limma documentation, testing for "main effect" and "interaction effect" is not a useful way to analyse a gene expression experiment. The above article explains a better way. It covers some of the same ground at the limma User's Guide but at greater length with more tutorial comments.