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picrust / picrust2

Code, unit tests, and tutorials for running PICRUSt2
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object 'p_values_df' not found (error) #310

Closed atozga closed 6 months ago

atozga commented 1 year ago

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_valuesdf' 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 = "pathwayname", select = NULL, reference = NULL )

atozga commented 1 year ago

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.

gavinmdouglas commented 1 year ago

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