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`DESeq2` is a package design to use it for RNAseq data, but also you can use this library with metabarcoding data. I want to use `DESeq2` package to find OTUs that differ in categorical variables. The…
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Hi,
I read that several OTU tables can be combined into one, but that this is not necessary if the combined output is to be input again into summarise. My question is whether I can? Can I use a com…
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Hello,
I have a subsetted phyloseq object "x", containing 9 taxa.
I've created relative abundances of the read data (using ```microbiome::```), so when running ```otu_table(x)``` I get relative…
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I don't know why but phyloseq allows two kind of otu layout in a phyloseq object; one is taxa_are_row and the other one not. To access this information, one can use taxa_are_row(phyobj) to check.
W…
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Hello, I am currently using microViz for beta diversity analysis with OTUID, OTU_ID, taxonomy, and sampleid data from txt files. I tried running the following script to obtain my phyloseq files:
```r…
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The taxon_ids that are present in the otu_table/tax_data tables are different, but related to the taxon_ids in the tax_table/diff_tables created by coercing the phyloseq object into a taxmap object as…
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Hi,
Thanks for developing this package.
I was trying to use this package and was stuck for a long time to figure out an error:
`r$> result_HILIC
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Hello,
I tried to apply your script on my data.
My phyloseq object looks like this:
phyloseq-class experiment-level object
otu_table() OTU Table: [ 85 taxa and 27 samples ]
sample_data…
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Dear Joey,
I am trying to make some ordination plots on my data, but I always encounter errors when I use `type = "samples"` using plot_ordination.
`> mydata`
`phyloseq-class experiment-level object…
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HI, I have been trying to create "physeq" and encountered the following error while loading the TAX table.
Error in (function (classes, fdef, mtable) :
unable to find an inherited method for f…