Microbiome Data Format for OmicsAnalyst


I have questions about the 16S microbiome data format for the OmicsAnalyst.

My plan is to run data integration with the transcriptome and the microbiome (from 16S amplicon) data from the same experiment.

Both the metadata and the transcriptome data were uploaded without issues. The microbiome file was uploaded and parsed successfully. But 2 error messages showed up. 1. check the taxonomy. 2. check the missing values.

I compared my own data to the example" mouse colitis" data from your site and could not figure out where the problems are.

Then I tried replacing the taxonomy column by the OTU numbers and rerun the upload process. This time the “taxonomy” error message disappeared but an empty “error” box still popped up without further information.

The microbiome file is attached.

I have both the taxonomy and the OTU information left on the table for your convenience. Could you please help?

Thank you so much for your assistance!

A follow-up question is, with the metadata already uploaded in OmicsAnalyst, is it necessary to include environmental or experimental conditions in the microbiome data table, or are the sample IDs matching the metadata sufficient for analysis?

Thank you,

Hello, you don’t need add experimental conditions in microbiome data table as the information has been provided by metadata file. And you can only include one column as #NAME to identify the features. You can either use the taxonomy or the OTU ID. Make sure the IDs are unique.
Hope this helps!

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Hi Yao,

Thank you so much for your response. I will test what you suggested over the weekend.

In the meantime, could you please remove my microbiome data from the message above or let me know how to do it from my end? Thanks again.

Hi Yao,

Thanks for removing the data file attachment from the above message.

I changed several things on my data table today:

  1. removed conditions as you suggested.
  2. replaced hyphen “-” by underscore “_” for the taxonomy labels.
  3. switched feature labels between the taxonomy or OTU

None of the above modifications worked. I am still seeing the same 2 error messages

1. Check the taxonomy labels
2. Missing values detected.

I checked missing values using another statistical software “JMP”. No missing value was detected in my file. Next, I copied the taxonomy labels from the example “mouse colitis” file to replace my own labels just for a try. I even tested the “mouse colitis” file directly on the OmicsAnalyst.

The error messages did not go away even though the microbiome files were uploaded and parsed successfully. The “Proceed” button did not generate integration results.

Could you please check my modified file?

16S_Clean.csv (112.9 KB)

Thank you so much! :pray:

Hello everyone. I am new to this community, and I wanted to express my gratitude to the team of experts who volunteer their time to help others. I recently posted a question about the microbiome data format. Although my last reply was sent to Yao, I would appreciate any help from anyone with expertise in this area.

Thank you all again for your kindness and support!

Good Morning All,

I was able to upload my 16S data by not specifying data type. The autoscaling
went well. Then I was not able to run the “identifying significant features with complex metadata”. An error box popped up without further explaination. I tested running the process with example datasets without any problem.

Attached are the files used, and the screenshot of my error page.

[MODERATOR EDIT: data removed at request of user]

Your kind help for troubleshooting is greatly appreciated.

Thank you.

Dear Andie1,

I have updated the website so that it can handle your dataset for comparison analysis, can you try again?


Hi Guangyan,

Yes, it is working now. I was able to finish the comparison analysis for the first time.

Thank you so much again for your help!!

Hi Guangyan,

Could you please remove the 3 attached files in the message above for me?

Thank you very much for your assistance, :pray:

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