Help with merging replicates for sequence data in Phyloseq. I've been stuck on this for months. ):


I am using the R package Phyloseq to analyze data. I have two sample types that have unequal replicate sizes but I want to combine the replicates together to make one sample containing the OTU abudnance and respective taxonomy and the sample name form the meta data. I have tried the merge_samples() function in Phyloseq but it hasn't worked for me. Does anyone have any suggestions?



In order for us to help you with your question, please provide us a minimal reproducible example where you provide a minimal (dummy) dataset and code that can recreate the issue. Once we have that, we can go from there. For help on creating a Reprex, see this guide:

Good luck!

Have you gone through this ?
Merge Data (
it might be a way for you to compare what you have to what the examples used look like

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