To Whom It May Concern,
Using DEXSeq, I am attempting to run an analysis of differentially used exons between two treatments groups at different False Discovery Rates (10%, 5%, and 1%). Yet the commands for running the test (
testForDEU ) and retrieving results (
DEXSeqResults) seem to have no argument for alternative FDR's. In the manual, It seems that only running HTML reports supplies an argument for this. Am I missing something where I can run three separate tests that also correspond to matching adjusted p value thresholds?
Results_from_test_10: FDR of 10% with Differentially used exons < 0.10
Results_from_test_05: FDR of 5% with Diff used exons < 0.05
Results_from_test_01: FDR of 1% with Diff used econs < 0.01
Thank you for your time!