More than 2 conditions in dfAnnotation to compare

[lovebaboon1989]

Hi there,
I am currently dealing with a RNA seq dataset in which I have 2*2 conditions, so I just wonder if there is any method or option to manually define which condition is 'case', which condition is 'control' to help me get the impulseDE genes. I noticed that in previous version 'ImpulseDE', there was an option to mannually define this but do not find this option in 'ImpulseDE2'. Thanks a lot!

[davidsebfischer]

Our statistical test only allows for two group comparisons, my first thoughts would be:

1. Is one of these conditions potentially a confounder (batch) and you can dervive insight from looking at the other condition, corrected for this effect?
2. Multiple pariwise fits or fits in isolation if you care about DE genes across time in each condition and want to start doing analyses from that point onwards.

[lovebaboon1989]

Hi David,
Thanks a lot for your reply, I would try split the samples and do pairwise comparison for each condition.