Open aff30 opened 2 years ago
Hi @aff30
Is pst
an phyloseq object? What is the message shown in R when you type in pst
and dim(otu_table(pst))
Hi - when I type pst I get: phyloseq-class experiment-level object otu_table() OTU Table: [ 8897 taxa and 614 samples ] sample_data() Sample Data: [ 614 samples by 4 sample variables ] tax_table() Taxonomy Table: [ 8897 taxa by 6 taxonomic ranks ]
and, dim(otu_table(pst)) [1] 614 8897
Thank you!
Hi, I am new to the microbiome analysis and I have been trying to filter my microbiome data after decontam but have encountered some errors. I am in the part where I would like to remove taxa with a total relative abundance of less than 10e-5 using the following code and getting the following error below:
Error in validObject(.Object) : invalid class “otu_table” object: OTU abundance data must have non-zero dimensions.
I understand that it is filtering everything but I don't know how to change it. Could you help me with that? Thank you so much