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?
Example:
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
You can subset the results class with any cuttoff you like, as the results object has a "padj" column, which contains the the adjusted p value (also known as the FDR adjusted p-value), by some multiple testing adjustment, here using the Benjamini-Hochberg method.
At the end of chapter 4 of the vignette you will see how to do this:
table( dxr2$padj < 0.1 )
This will give you the number of DEU with a 10% FDR cutoff. Change that to 0.05 for 5% and 0.01 for 1%. If you want to get the subset of results object that meet that FDR cutoff I think something like this should work:
dxr2sig <- dxr2[ which(dxr2$padj < 0.01 ), ]
I am not sure what you mean by "FDR of 10% with Differentially used exons < 0.10" and by "three separate tests", as the differential exon usage test here is only run once, you are just exploring different arbitrary FDR cutoffs?
