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otu_table from phyloseq object does not have correct abundance: all asv are "0" for specific group of samples

This question was also asked on stack overflow I have QIIME2 outputs (feature table, tree, taxonomy, and metadata) that I've imported into R using qiime2R (v. 0.99.6) ‘qza_to_phyloseq’ to create a ...
Geomicro's user avatar
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I want to know what are the main differences between two R Objects constructed for analysis of microbiome data: phyloseq and TreeSummarizedExperiment

I am looking for main differences between two R Objects constructed for analysis of microbiome data: phyloseq object and TreeSummarizedExperiment object First, I will provide a little information ...
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Try to understand better how to set out an effective sample size within the MetagenomSeq package in microbiome

Cross-posted on biostars: https://www.biostars.org/p/9572744/ I am trying to understand better what number to be used and how to put it in the function MRcoefs within the Metagenomeseq package in R ...
Mohamed Samir's user avatar