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Hi Huang,
I am trying to run pairwise comparisons on 4 groups (for example, Comparison 1 groups = A, B, C, D) using ANCOMBC2 and I get this error message:
Error in names(y)
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So, I am running ANCOMBC2 on a phyloseq object and I am seeing this warning thrown multiple times:
> In lme4::lmer(formula = tformula, data = df, control = lme_control) : restarting interrupted pr…
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Hello,
I wonder if `ancombc2()` could analyze ASV or OTU-level abundance table and GENE or PATHWAY level abundance table (from shotgun metagenome analysis).
In my test running of `ancombc2()`, `…
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Hi,
I am actually trying to run ANCOMBC from a phyloseq object but I always get the same error message and I do not know what is the problem. I want to see the difference bacterial abundance between …
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I am having an issue which I am not able to solve. The error is located in the `iter_remle()` function and its due to wrong colum names assignment.
I am running ANCOMBC_2.1.1. I can't replicate the…
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Hi,
I had analyzed my data using `ancomb` function and now wanted to use `ancombc2` as I want to do pairwise comparisons. However, when I try running the function, I get the following error:
> E…
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Hi,
I need to rerun some analyses performed before the new version of ANCOM and I am not able to do so. I am told ANCOM-BC is deprecated. Is there a way to perform analyses as they were in ANCOM-BC a…
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Hi @FrederickHuangLin
I have seen the package and I find it very interesting. I have to do an analysis with longitudinal data and wanted to ask if there is any date for the new release containing l…
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I noticed with my own data that if I try to include a random intercept for subject, `rand_formula = "(1|Subject)"`, the `res` table in the output has all zeros in the lfc columns, a constant value aro…
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https://github.com/FrederickHuangLin/ANCOMBC/blob/dbf4fb5c1434b551b087644836596a05f9660780/R/ancombc_prep.R#L98
Hello!
Here is a bug. `altExp` should be specified by `altExp(tse, "something")`. …