object 'p_values_df' not found (error)

[Andrew T Ozga]

Hello,
I encountered the following error and I'm not seeing any posts about it:

The kegg pathway with zero abundance in all the different samples has been removed.
Error in pathway_daa(abundance = abundance, metadata = metadata, group = group, :
object 'p_values_df' not found

Could this be something with my file format/code or is there another input component i need to include? Thank you.

FNmeta<-read_delim("FN_Meta.tsv", delim = "\t", escape_double = FALSE)
group<- "site"
daa_results_list<- ggpicrust2(
file = "pred_metagenome_unstrat.tsv",
metadata = FNmeta,
daa_method = "linDA",
group = "site",
pathway = "KO",
p_values_bar = TRUE,
ko_to_kegg = TRUE,
order = "pathway_class",
x_lab = "pathway_name",
select = NULL,
reference = NULL
)

[Andrew T Ozga]

Sorry I realize this is associated with the ggpicrust2 package within R, but I wanted to submit this here in case someone has encountered the problem after initial picrust usage.

[Gavin Douglas]

Hi there,

I can leave this up here for a while, but it's not an 'issue' for this repository. You can try posting in the picrust-users forum too to see if anyone has run into similar problems: https://groups.google.com/g/picrust-users?pli=1

Cheers,

Gavin