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cafferychen777 / ggpicrust2

Make Picrust2 Output Analysis and Visualization Easier
https://cafferychen777.github.io/ggpicrust2/
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pathway_daa() #89

Open manijehmahdavi opened 4 months ago

manijehmahdavi commented 4 months ago

Hello, I have a problem when I want to run this command: daa_results_df <- pathway_daa(abundance = kegg_abundance, metadata = metadata, group = "Environment", daa_method = "linDA", select = NULL, p.adjust = "BH", reference = NULL)

I got this error: Invalid differential abundance analysis method. Please choose from: ALDEx2, DESeq2, edgeR, limma voom, metagenomeSeq, LinDA, Maaslin2, Lefser

My question is how to input my DAA results in the ggpicrust analysis. I should do that? or is it not necessary? my DAA was based on ANCOM-BC. How can I solve this problem?

Best regards

cafferychen777 commented 4 months ago

Hello @manijehmahdavi,

Thank you for reaching out and using our package.

Currently, ggpicrust2 does not support ANCOM-BC, but we are keen on including this feature in future releases. In the meantime, I recommend you try using LinDA for your Differential Abundance Analysis (DAA). LinDA and ANCOM-BC share similar statistical principles, and it should serve as a suitable alternative for your analysis needs.

Regarding the integration of DAA results into ggpicrust analysis, it is not mandatory to input your DAA results. However, if you choose to use LinDA or any other supported method, you can proceed with the analysis as per the package's guidelines.

Please feel free to reach out if you encounter any further issues or have additional questions.

Best regards,

Chen YANG