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Hi Kai,
I get this error whenever I try these scripts in R:
> ps
phyloseq-class experiment-level object
otu_table() OTU Table: [ 1052 taxa and 24 samples ]
sample_data() Sample Data…
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Hi Joey
Would it be possible when creating phyloseq objects to report samples and OTUs lost?
This is more for project management purposes than for PhyloSeq purposes, but occasionally (quite often) p…
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Hello!
I'm trying to use aldex.glm() to explore differential abundance for a complex design involving both Genotype (B6 vs. TCR) and stress condition (Stress vs. NoStress). My code is as follows (d…
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Dear yijuanhu,
I would like to use the LDM package to analyze data processed by other normalization methods (e.g. CSS), do I need to add the following parameters in the `ldm()` function, such as:
`…
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Hi there,
I have sequenced both fungi (ITS) and bacteria (16S) for the same samples and now I want to merge the two phyloseqs together to look at co-occurance patterns between the two kingdoms. Is th…
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Congratulations on the publication and thank you for sharing your code and data!
I tried tab 'sTable8', 'sTable10' from the supplementary table in place of files "20190307_CR_NICU/201903_NICU_combi…
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Hi,
I'm using SourceTracker in R for the first time and can't work out an error I'm getting when using the sourcetracker() function on my own data (works for example data though):
Error in if (s…
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Good day,
I read your recent paper Zamkovaya et al 2021 in ISME and I am excited to implement a similar network analysis (mdmnets package) with my data, but I am running into issues at the start of …
dvc28 updated
2 years ago
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Hi!
when i make a phyloseq object like this:
``ps2
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Dear All,
I am trying to using mdine package for my analysis. My otu table contains 422 OTUs and 1547 samples. I have binary disease condition. I executed the following steps (after uploading the dat…