I very well realize the importance of replicates as well as your advice in this forum multiple times to other questions earlier that no meaningful statistics can be done without replicates.
However, the data I have received to analyze has bad replicates. There are three matched pairs for two conditions and the biologist says that they can be loosely considered as replicates, but the initial correlation heatmaps indicate that they are quite far apart. As a result, when I use DiffBind, I don't see more than 1 differential binding site with default FDR. So, I set
th=1 to get the full report.
However, my question is that if I wish to treat the three pairs separately, two at a time and just compare them without treating them as replicates, what can I do?
I see that the documentation for "dba.contrast" says the following:
minMembers when automatically generating contrasts, minimum number of unique samples in a group. Must be at least 2, as replicates are strongly advised. If you wish to do an analysis with no replicates, you can set the group1 and group2 parameters explicitly.
So, if I have just two samples, one per condition, is there a way to just get the output of fold changes? That is, process them using counts and then get the scores and outputs with fold changes? I can then potentially give these results to the biologist.
Any advice would be greatly appreciated.
Thanks a lot!