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cafferychen777 / ggpicrust2

Make Picrust2 Output Analysis and Visualization Easier
https://cafferychen777.github.io/ggpicrust2/
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Error in if (dispersion == 1) "LRT" else "scaled dev." : missing value where TRUE/FALSE needed #78

Open Selucote8223 opened 7 months ago

Selucote8223 commented 7 months ago

Dear Caffery Yang,

I followed the directions described in the workflow, but I got errors for both ALDEx2 and LinDA methods. My metadata file is as follow:

sample-id mat-colour year month day 0913CV_3C Yellow 2021 Dic Unknown 0913CV_5E Red 2021 Dic Unknown 0913CV_7G Yellow 2021 Dic Unknown 0913CV_11K White 2021 Dic Unknown

setting "sample-id" for "group" option when differential abundance analysis was performed.

For ALDEx2 method the error was as described in title:

Error in if (dispersion == 1) "LRT" else "scaled dev." : missing value where TRUE/FALSE needed

The error showed with LinDA was the following:

Error in [.data.frame(LinDA_metadata_df, , matching_columns) : undefined columns selected

Could you help me? please.

Thank you!!

cafferychen777 commented 7 months ago

Dear @Selucote8223,

Thank you for reaching out with your query regarding the ALDEx2 and LinDA methods errors. I appreciate the details you have provided.

I noticed that your metadata file contains only four samples. Could you please confirm if these four samples are the entirety of your dataset? In statistical terms, this might pose a challenge. Many differential abundance (DA) methods, including those you are trying to use, typically require a minimum of two samples per group to perform valid comparisons and analyses. This requirement is crucial for statistical validity and to ensure reliable results.

If your dataset indeed comprises only these four samples, this might be the root cause of the issues you are encountering. In such a scenario, adding more samples to each group or considering a method suitable for very small sample sizes might be necessary.

Looking forward to your confirmation and any further details you can provide, so we can assist you more effectively.

Best regards, Caffery Yang

Selucote8223 commented 7 months ago

Dear Caffery Yang,

Indeed, this seems to be the problem, as you highlighted. I'm going to try alternative analysis to fit results to my outputs.

Thank you!