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Hi, zqfang.
I recently learned of your GSEApy and immediately tried prerank with [the data I had on hand](https://github.com/searchlie/misc/blob/main/2022-08-16-test.rnk) and compared it to results o…
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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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from the [docs](https://gseapy.readthedocs.io/en/latest/gseapy_example.html?highlight=mouse#Mouse-gene-symbols-maps-to-Human,-or-vice-versa)
```
from gseapy import barplot, dotplot
dotplot(res.…
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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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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 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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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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I have run:
```
mmG
zhq90 updated
2 years ago
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Hi,
Can ALDEx2 be expanded to do post-hoc testing and report results of comparisons between multiple groups, like it does between two groups? For example, my project has 16 different treatments, an…
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Hello all,
I am working on a project using BUSTED-PH and RELAX to assess whether there are differences in (1) the genome-wide proportion of genes under positive selection in a group of species wit…