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One of the "problems" I'm having with metagenome graph-based differential abundance (implemented in #303) is that there are *a lot* of cDBG nodes, so even catlases built with R5 have *a lot* of domina…
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Hello!
I need instructions on how to model for mixed effects. For example, I want to perform a differential abundance analysis using LINDA algorithm modeling for 'Age + Sex + Batch + (my variable o…
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**Addition Description**
I have a use case where I would like to compute the ILR transform on an entire tensor of (samples) x (features) x (monte_carlo_estimates). Doing so would open the doors for …
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Hi,
Thank you for an excellent approach to functional metagenomics. I have a major concern with the normalization method based on relative abundance. It has been demonstrated that is one of the wor…
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Hello,
I'm experiencing an error while using DCATS for differential abundance testing with my single-cell data. Specifically, the error below occurs during the dcats_GLM step
`Error in if (it > mi…
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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 …
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I *think* some of the output fields you get from some tools (e.g. ALDEx2) aren't exactly log-fold changes -- stuff like the p-values included in the `FeatureData[Differential]` output (e.g. `we.ep`) m…
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Hi all,
I am having a lot of issues with MicrobiomeSeq.
Here are some example of errors I am getting:
`kw_sig
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This is a new warning being generated by the tests, and I don't think there are actually should be collinear variables here so I'm not sure what's happening.
``` r
suppressPackageStartupMessages(l…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/feargalr/TaxSEA
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