Phylogenetic tree in phyloseq object

microEcology / pime

PIME: A package for discovery of novel differences among microbial communities

GNU General Public License v3.0

5 stars 2 forks source link

Phylogenetic tree in phyloseq object #1

Open Alishumali opened 5 years ago

Alishumali commented 5 years ago

Hi, PIME has been an amazing addition to the microbiome analysis tools I use, thank you for putting it together. I tried using PIME with a phyloseq object that has a tree attached and it doesn't allow it but when I remove the tree it runs well. I must've missed something in your tutorial, appreciate your help.

cheers, Alishum

Alishumali commented 5 years ago

Sorry i didn't include the error output. the command : prev <- pime.prevalence(per_variable_obj) the error: Error in FUN(X[[i]], ...) : one tree has a different number of tips

michael-nakai commented 4 years ago

I'm having a similar issue. When I run the command prevalences=pime.prevalence(per_variable_obj), I get the same error. However, removing the tree allows the command to run. What exactly is happening here?