Background Selection for Enrichment Analysis in IsoformSwitchAnalyzeR

[Faizan Rashid]

Hi,

I have been using IsoformSwitchAnalyzeR and found it to be extremely useful for analyzing alternative splicing events. However, I have some questions regarding background selection for performing over-representation analysis, particularly for genes in each alternative splicing category as well as for all genes with significant isoform switches.

I plan to use DAVID for enrichment analysis and wanted to clarify the appropriate background list to use from  IsoformSwitchAnalyzeR  . My current understanding is to select the background from the genes after initial filtering (i.e., filtering for low read counts) but before applying any cutoffs for isoform switching significance.

Could you please confirm if this is the correct approach? If not, could you suggest an alternative background and explain how I might retrieve this background list from IsoformSwitchAnalyzeR?

Thank you in advance for your guidance.

Best regards,
Faizan Rashid