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joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
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otu_table not only numeric? Estimate_richness /plot_richness doesnt work - how to troubleshoot? #1666

Open mariamaseng opened 1 year ago

mariamaseng commented 1 year ago

Hi! I have a phyloseq object, and want to estimate richness. I am getting the error message printed below, and that makes me suspect that my otu table isnt interpreted as only numeric values. I have done validate_phyloseq(), and it seems good. Got any tips on how I should go about troubleshooting this? Fyi I transformed it (by makeTreeSummarizedExperimentFromPhyloseq) into a tse-object and did estimateDiversity and it works.

Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 't': function accepts only integers (counts)

mariamaseng commented 1 year ago

Update: I think I know what it is. I do have many not whole numbers (0.3333) in my otu-table. Suspect that to cause the problem.