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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…
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Dear Guangchuang.
I've been running some side-by-side comparisons of GSEA-P and gseGO from clusterProfiler, using the same ranked-by-logFC list of genes.
I am linking to two corresponding analysis f…
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Hi Nic, cool stuff.
Having a quick read through it and I think it could be useful to correct the alpha level for multiple testing (as you may have panels with hundreds of SNVs).
Another questio…
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Hi GOfuncR contributors,
I have question about this tool. I am working on enrichment analysis for a geneset and tried to run the "refine" function from the GOfuncR package. I noticed that different…
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I am calling variants the most recent version of Sniffles, HG002 ONT ultralong reads from GIAB aligned with minimap2 to b37 reference (ftp://ftp.ncbi.nlm.nih.gov/1000genomes/ftp/technical/reference/hu…
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Hello and thank you for the very useful tool,
I would be happy for your insight regarding two issues:
1. I have >2 phenotypes, "categorical" groups. How to deal with such data in PySEER? It only…