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EC details iHMP_metabolomics

We are planning to use metabolomics and metagenomics data from the IBD dataset in our project.

I have downloaded the metabolomic file named as “iHMP_metabolomics” from the link /products/HMP2/MBX and the metagenomic file “ecs_relab.slim” from the link /products/HMP2/MGX through the FTP server. I could not find detailed information about the values of these data files in the paper.

For both of the data files have you performed transformation/normalization? Can I use these values without any normalization step for performing the analysis? For example, In “iHMP_metabolomics” file, the values are too high, In “ecs_relab.slim” file, there are too many zero values, what does the zero mean? Is it that the enzyme does not exist in the related sample.

Hi user,

The transformation/normalization for the data files are dataset-specific (for e.g. the ECs are different from the MBX.)

Metagenomics(MGX) samples ran through HUMAnN pipelines generating the ECs from UniRefs. (MGX -> HUMAnN -> UniRefs -> ECs)

Metabolomics(MBX) samples are normalized separately by different methods then combined.

Regards,
Sagun

Dear Sagun,

Thank you for your reply.
I have some questions; I would be appreciated if you answer them

  1. In “iHMP_metabolomics” file, the values are too high, How are these values be normalized? Should I use them without any preprocessing in my statistical analysis?

  2. In “ecs_relab.slim” file, there are too many zero values, what does the zero mean? Is it that the enzyme does not exist in the related sample.