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waldronlab / lefser

R implementation of the LEfSe method
https://waldronlab.io/lefser/
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Error in cols * 0.05 : non-numeric argument to binary operator #24

Closed chuynh96 closed 3 weeks ago

chuynh96 commented 11 months ago

Hello,

I was able to convert my phyloseq object (output from the DADA2 pipeline) into a SummarizedExperiment object such that it mirrors the example SummarizedExperiment from the vignette (zeller14). However, using lefser(MySE, groupCol = "study_condition"), I keep getting this error: Error in cols * 0.05 : non-numeric argument to binary operator

I have no idea why I'm getting this error! I also attempted to use relative abundance rather than raw counts (although it appears the example zeller14 SummarizedExperiment just has raw counts) to see if it would prevent the error, to no avail.

Any advice anyone?

asyakhl commented 10 months ago

Hi @chuynh96, cols is a numeric vector, which has your abundance values per feature. I would check that all of your abundance values are numeric. Or check that MySE is set up similarly to assay(zeller14). If that doesn't resolve this issue, could you point me to your dataset and conditions with which you run lefser.

LiNk-NY commented 10 months ago

@chuynh96 Any updates on this?

lwaldron commented 3 weeks ago

Closing as error is not reproducible.