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ahmohamed / lipidr

Data Mining and Analysis of Lipidomics datasets in R
https://www.lipidr.org/
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lsea issue #18

Closed garodriguezblanco closed 3 years ago

garodriguezblanco commented 3 years ago

Hi there, I'm getting the following error, even with the breast cancer dataset. Any idea how to fix it? thanks in advance

enrich_results = lsea(two_group, rank.by = "logFC") Error in fgsea::fgsea(pathways = pathways, stats = stats, minSize = minSize, : argument "nperm" is missing, with no default In addition: Warning message: In fgsea::fgsea(pathways = pathways, stats = stats, minSize = minSize, : There are ties in the preranked stats (9.04% of the list). The order of those tied genes will be arbitrary, which may produce unexpected results.

ahmohamed commented 3 years ago

Hi @garodriguezblanco, fgsea modified the function signature in the last release. Just update fgsea and it should work fine.

ahmohamed commented 3 years ago

Closing the issue. Feel free to open if needed.

garodriguezblanco commented 3 years ago

Thanks for your help! it is working nicely now. Gio

On Thu, 4 Feb 2021 at 21:38, Ahmed Mohamed notifications@github.com wrote:

Hi @garodriguezblanco https://github.com/garodriguezblanco, fgsea modified the function signature in the last release. Just update fgsea and it should work fine.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ahmohamed/lipidr/issues/18#issuecomment-773620045, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASXLE5DPCA6BUVEMP6TAPT3S5MHTXANCNFSM4XDHQGCA .

-- Giovanny Rodríguez-Blanco PhD

Mass Spectrometry

Edinburgh CRUK Centre

Institute of Genetics and Molecular Medicine

University of Edinburgh