How to run diff_iso_usage with multiple samples per condition?

[evans-ZH]

I have multiple biological replicates per condition. Can diff_iso_usage be applied to all replicates from two conditions simultaneously?

From the documentation, it appears that diff_iso_usage is primarily designed for pairwise (two-sample) comparisons, so I am unsure how replicates should be handled.

Thanks for the clarification.

[cafelton]

diff_iso_usage is our secondary splicing analysis function, only for cases without replicates. Running flair diffexp will give you drimseq results comparing isoform usage between groups with replicates

[hyl2509]

diff_iso_usage is our secondary splicing analysis function, only for cases without replicates. Running flair diffexp will give you drimseq results comparing isoform usage between groups with replicates

How can I analyze differential isoform usage if I only have two replicates per condition?

[cafelton]

This is a little clunky, but what I've done in the past is run diff_iso_usage on each pairwise comparison of condition A and B (4 comparisons), then taken the maximum p-value and minimum delta-PSI across all comparisons for each event.