PicRust2 Error : number of statistically significant pathways exceeds the database's query limit. about picrust2 HOT 5 CLOSED

#Update:
I was able to run LinDA using-
ko_abundance <- "feature-table-ko.tsv"
kegg_abundance <- ko2kegg_abundance(file = ko_abundance)
but still kind of same error with no annotated pathway in the table.

from picrust2.

I'm afraid that I'm not familiar with ggpicrust2 as it was made by different developers and I haven't personally used it. You could try asking this question in their github page here?

from picrust2.

Hello,

Firstly, I would like to extend my gratitude to the PICRUSt2 developer and maintainers @R-Wright-1 for their hard work on the tool and for pointing you to the right direction.

@sm-arosh,
Thank you for reaching out with your concern. I understand the error you've encountered while using ggpicrust2. To help address this, I'd recommend you follow the troubleshooting workflow provided in the ggpicrust2 documentation. You can find it here: https://github.com/cafferychen777/ggpicrust2#if-an-error-occurs-with-ggpicrust2-please-use-the-following-workflow.

After trying the suggested workflow, if the issue persists, please let me know and provide more details if possible. I'm here to assist you.

Best regards,

Chen YANG

from picrust2.

Hello, I was trying to use ggpicrust2 in order to assess differentially abundant pathways predicted by picryst. It all ran fine and gave this error in the end. I'm attaching the files I used and hoping that someone can assist me on how to solve this. I couldn't find any parameter to increase the p-value to 0.01, so I'm lost on how to overcome this. I'm adding the links to the files that I used and also the code. ko : https://drive.google.com/file/d/1UBDAXcxRg_ypo2JjfVY4nAAP9fW4g2E2/view?usp=sharing metadata: https://drive.google.com/file/d/1swls-F91PiHfqsnjqIJQ7H2MpqTlVz7l/view?usp=sharing

Code: kegg_abundance <- "feature-table-ko-new.csv" metadata <- read_tsv("metadata_final.tsv") results_file_input <- ggpicrust2(file = kegg_abundance, metadata = metadata, group = "Diabetes_typ", pathway = "KO", daa_method = "Maaslin2", ko_to_kegg = TRUE, p.adjust = "fdr", order = "pathway_class", p_values_bar = TRUE, #reference = "ND", x_lab = "pathway_name")

Hey
Excuse me, have you solved this problem?

from picrust2.

I'm just closing this issue here as it related to ggpicrust2 and not PICRUSt2. Thanks @cafferychen777 for keeping an eye on here, too!

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