DiffBind package showing warnings and unable to analyse my data

Question

[chaudharyc61]

Hello everyone

I am using DiffBind Bio-conductor for differential binding analysis. I have four replicates of same experiment so the Condition column is same for all the replicates, while getting the contrast in R (i.e My_data <- dba.contrat(My_data, categories = DBA_CONDITION) ) I am getting warning :

Warning message: No contrasts added. Perhaps try more categories, or lower value for minMembers.

I tried changing minMemebers and also the categories but still the same error is coming. Please Help

Thank you...

Answer 1

[Rory Stark]

What are the sample groups that you are trying to find the difference between? If all four samples are replicates of the same sample type, there is nothing to contrast.

Another way to look at this: if all the samples have the same values for the Condition, what other attribute (Tissue, Factor, Treatment) do they have different values for?