PicRust2 Error : number of statistically significant pathways exceeds the database's query limit.
sm-arosh opened this issue · comments
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")
#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.
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?
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
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?
I'm just closing this issue here as it related to ggpicrust2 and not PICRUSt2. Thanks @cafferychen777 for keeping an eye on here, too!