Tag: ASVs

Phyloseq Objects for different time points

Phyloseq Objects for different time points 0 Hi I am very new to this microbiome analysis so this might be a very simple question… I have a question related to the microbiome analysis I’m doing. I have microbiome data from 3 different timepoints (T1, T7, and T13), for I made…

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How to get normalized count table from DESeq?

How to get normalized count table from DESeq? 1 Hi, I’m using Deseq compare differential abundance. Here is my code: ds.all <- phyloseq_to_deseq2(ps0.infant.pbs, ~ sample_type) geoMeans <- apply(counts(ds.all),1,gm_mean) ds.all <- estimateSizeFactors(ds.all,geoMeans = geoMeans) dds.all <- DESeq(ds.all,fitType = “local”) Then as the results I got 8 ASVs that showed significantly different….

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Relative abundance of differentially abundant ASVs after DESeq2

Relative abundance of differentially abundant ASVs after DESeq2 0 Hello, I used DESeq2 to see which ASVs were differentially abundant between different treatments on 16S metabarcoding data. I now want to plot the relative abundance (in %) of those ASVs. However, I am unsure which data would make to most…

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