error in filter function after upgrading R version

General
#1

Hello everyone,

I'm using the function phyloseq_filter_prevalence to filter a phyloseq object using R version 4.2.3 and it's working correctly with me, when I upgraded R version to v. 4.3.1 I got an error "OTU abundance data must have non-zero dimensions" with the same data,
R version was switched to the old version 4.2.3 to check again and it worked
the command:

physeq3 <- phyloseq_filter_prevalence(physeq.gen, prev.trh = 0.5, abund.trh = 10, threshold_condition = "OR")
Error in validObject(.Object) : invalid class “otu_table” object:
OTU abundance data must have non-zero dimensions.

I appreciate any suggestions in advance
thanks

#2

It sounds like you are using the phyloseq package (from BioConductor)? If so, you might consider posting in a BioConductor-specific forum instead, or if you are convinced there is a bug, at the github tracker: Issues · joey711/phyloseq · GitHub

1 Like
#3

Hi @btyner
thanks for your suggestions
regards!