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

[price793]

Hi,

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?

Best

[pieterjanvc]

Hi,

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:

FAQ: How to do a minimal reproducible example ( reprex ) for beginners

A minimal reproducible example consists of the following items: A minimal dataset, necessary to reproduce the issue The minimal runnable code necessary to reproduce the issue, which can be run on the given dataset, and including the necessary information on the used packages. Let's quickly go over each one of these with examples: Minimal Dataset (Sample Data) You need to provide a data frame that is small enough to be (reasonably) pasted on a post, but big enough to reproduce your issue. Let's say, as an example, that you are working with the iris data frame head(iris) #> Sepal.Length Sepal.Width Petal.Length Petal.Width Species #> 1 5.1 3.5 1.4 0.…

Good luck!
PJ

[nirgrahamuk]

Have you gone through this ?
Merge Data (joey711.github.io)
it might be a way for you to compare what you have to what the examples used look like