When you run dba.contrast and dba.analyze in DiffBind, it divides the samples into all the possible groups and compares the various groups. If you have paired samples (for example, before and after treatment), is there a way to indicate that so that the analysis takes that into account (rather than simply doing all "before" versus all "after")?
Hi,
The block parameter of dba.contrast allows the sort of paired comparison you want. See section 5 of the vignette for details.
The block parameter is set up to handle paired samples. So for example if the CONDITION is before or after, and each pair of samples share the same REPLICATE or TISSUE id, you can try:
myDBA <- dba.contrast(myDBA, group1=myDBA$masks$before, group2=myDBA$masks$after, name1="before",name2="after", block=DBA_REPLICATE)
myDBA <- dba.analyze(myDBA)
myReport <- dba.report(myDBA, method=DBA_EDGER_BLOCK)
Quick followup. This is your example:
dba.contrast(myDBA, group1=myDBA$masks$before, group2=myDBA$masks$after, name1="before",name2="after", block=DBA_REPLICATE)
Since we only have 2 conditions here, I would do this:
dba.contrast(myDBA, categories=DBA_CONDITION, block=DBA_REPLICATE)
Since you used the less concise approach, are the two actually different? Or was it to make the answer more clear?
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version 2.3.6
I looked at the block parameter. That seems appropriate, but it's fairly flexible. I wasn't sure if there is some other option that specifically assumes paired analysis.
To the best of my knowledge,
blockis the only parameter for this purpose. The EdgeR user manual gives a bit more detail about how to use it.