Microbiome and metabolome integration - file upload

OmicsAnalyst
1

Hello, I’m trying to use OmicsAnalyst to visualise together my microbiome data with my metabolomics data. I’m a bit unsure what the correct format my CSVs should be in, as the different combinations of files that I try to upload don’t seem to work. I’ve tried uploading the separate taxonomy and OTU data from my microbiome sequencing and also uploading my metabolomics concentrations, but the system doesn’t seem to like this.
concentrations samples as columns ST label.csv (34.2 KB)

METADATA.csv (1.1 KB)
OTU.csv (33.9 KB)
TAXONOMY.csv (23.5 KB)

I created a phyloseq object in R to help combine my taxonomy, metadata and OTU data from the microbiome sequencing and have managed to export this as a csv (phyloseq1.csv (1.5 MB)). I thought maybe this would work better and tried to upload this with my metabolomics concentrations, but to no avail. I keep getting errors such as “Error: a total of 267 samples and 54 features were found”.

Is anyone able to give me some help as to what layout my files should actually be in in order for it to work, as whatever I’ve tried has so far been unsuccessful.

Many thanks,
Daisy

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Please carefully read and follow our post guide

3

Hello,
I’ve updated my original post to include the relevant files I am referring to

4

Two comments:

  1. For multi-omics integration, a basic requirement is that different omics data will share the same sample names - this is not the case in your metabolomics data and microbiome data - see our Nature Protocol - Box 1

  2. You may want to try MicrobiomeAnalyst (instead of OmicsAnalyst) - which has a module dedicated for microbiome and metabolomics data integration - see MicrobiomeAnalyst 2.0 - Integrative analysis for data from microbiome metabolomics studies

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Thank you, I will try both of these options.
If I were to fix the sample names so that they match, would it be best to use the phyloseq object dataframe with the metabolomics concentrations, or should I upload the taxonomy and OTU separate files?

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