Question

accounting for gene length with SeqGSEA

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Julie Leonard ▴ 110

@julie-leonard-5222

Last seen 9.7 years ago

Hello- I've been working with SeqGSEA and I was wondering if there were plans to add the ability to account for gene length similar to how it's done in GOseq. Thanks, Julie Julie Leonard Computational Biologist Global Bioinformatics Syngenta Biotechnology, Inc. 3054 E. Cornwallis Rd. Research Triangle Park, NC 27709 USA phone 1-919-281-7449 julie.leonard@syngenta.com<mailto:julie.leonard@syngenta.com> www.syngenta.com<http: www.syngenta.com=""/> This message may contain confidential information. If yo...{{dropped:7}}

goseq SeqGSEA goseq SeqGSEA • 1.2k views

ADD COMMENT • link updated 8.5 years ago by Xi Wang • 0 • written 10.9 years ago by Julie Leonard ▴ 110

score 0 · Answer 1 · 2015-11-19

Hi Julie,

With sample permutation, we have not found obvious gene-length bias of the stats we used for gene set enrichment analysis. See Supplementary Figures S4-6. Such bias was believed to be cancelled out by permutation, so we don't need additional efforts to adjust for gene length or read counts.

Cheers

Xi