Hi,

I would like to find differential binding between tissue ct1 condition 1 and tissue ct1 condition 2. How might I set this up in the contrast statement? Thank you!

My sample sheet looks something like this:

ID   Tissue Condition Replicate
1   ct1        1         1 counts   
2  ct1        1         2 counts    
3  ct1        2         1 counts    
4  ct1        2         2 counts   
5  ct1     3         1 counts    
6  ct1     3         2 counts    
7   ct2        1         1 counts    
8   ct2        1         2 counts    
9   ct2        2         1 counts    
10  ct2        2         2 counts    
11  ct2     3         1 counts    
12  ct2     3         2 counts   

There are a couple of ways to do this.

You can generate all the contrasts automatically with dba.contrast(), but since you only have two replicates for each condition/tissue pair, you have to specify minMembers=2:

> myDBA <- dba.contrast(myDBA, categories=c(DBA_TISSUE,DBA_CONDITION), minMembers=2)

This will give you quite a few contrasts, including ones you probably don't need.

The second way is to specify each desired contrast explicitly:

> myDBA <- dba.contrast(myDBA,
                        group1=myDBA$masks$ct1&myDBA$masks$1, 
                        group2=myDBA$masks$ct1&myDBA$masks$2,
                        name1="Ct1 Cond1", name2="Ct2 Cond2")

​I'm not 100% sure will work with your condition names, you could also specify the samples directly:

> myDBA <- dba.contrast(myDBA,group1=1:2, group2=3:4,
                        name1="Ct1 Cond1", name2="Ct2 Cond2")