Hi,

I have three conditions in my data

1. Temperature (30C and 37C)
2. Media(YPD, YPD-CFW, YPD-EGTA, YPD-EGTA-CFW)
3. FLC1(Wild-Type and Delta)

I want to construct a design experiment to answer the question of how gene expression differs in all conditions. Also, I want to add the interaction, if possible, to the model. How to decide the appropriate model in my case? I was wondering what the criteria or metric could be used to choose the appropriate design.

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( )

There are a lot of kinds of questions you could ask with this data, but not all of them will necessarily be interesting.

You are probably going to want to run DESeq with a few different designs to answer all the possible ways you could compare different types of samples.

For instance, you might want a concatenated column with all the variables to compare subsets to subsets, and various kinds of interactions to answer others.