If I want to asses the overlapping between:

Differential binding sites between T1 and T2 (Control samples (untreated)) independent of the mouse type

> myDBA = dba.contrast(myDBA, group1=myDBA$masks$T1, group2=myDBA$masks$T2, block=DBA_CONDITION, name1="T1", name2="T2")

And differential binding sites of T1 taking into account the mouse type
> myDBA = dba.contrast(myDBA, group1=myDBA$masks$T1 & myDBA$masks$WT, group2=myDBA$masks$T1 & myDBA$masks$Transgenic, name1="WT:T1", name2="Transgenic:T1")

Should I proceed directly with :

dba.overlap(myDBA, group1=myDBA$masks$T1, group2=myDBA$masks$T2, mode=DBA_OLAP_RATE)

dba.overlap(myDBA, group1=myDBA$masks$T1 & myDBA$masks$WT, group2=myDBA$masks$T1 & myDBA$masks$Transgenic, name1="WT:T1", name2="Transgenic:T1", mode=DBA_OLAP_RATE)

Sorry , maybe it is really naive, but I think that I should maybe generate two different objects? I am a bit lost.

How many combinations I can do to after plot into a Venn Diagram? Is there a limit?

Thanks in advance!!

Sergio, did this get answered or are you still waiting for a response?

-Rory

Yes Rory, everything ok. Thanks a lot! 

Sergio