I am performing DiffBind on ATACseq data and I have a question regarding the use of block and design in setting a dba.contrast. From a previous question a couple of years ago I learned how to use block (DiffBind paired samples) but I think it might be different now in the new version as the design setting has changed.
I would like to block for replicate (or individual patient in my case) whilst also using a design that includes Tissue as confounder: ~Tissue + Condition. However, when I do that it says that block is ignored when design is used. Should I just include replicate in my design instead of as block or is there another way to analyze my data in a paired way while also including confounders in the design?
Data <- dba.contrast(Data, block = DBA_REPLICATE, design = "~Tissue + Condition", reorderMeta = list(Condition = "Isolated")) Output: Computing results names... Warning message: block ignored when design is used.
Many thanks for any help!