Batch Effect Correction Error Formatting Troubleshooting

MetaboAnalyst
1

Tool: MetaboAnalyst 6.0 web platform

Module: Batch Effect Correction (single merged file upload)

Issue: All batch correction methods return “Your data is not eligible for this method!” for every method including Automatic, ComBat, EigenMS, etc.

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This appears to be the same issue reported here: https://omicsforum.ca/t/batch-correction-issues-even-examples-not-eligible/13751

I spent time troubleshooting the formatting of my data file and have ruled out the following as potential causes:

  1. No spaces in feature names or sample IDs
  2. Feature names coded as numbers to avoid any naming conflicts
  3. No missing values
  4. No duplicate feature names
  5. Tried both “Sample in rows” and “Sample in columns” upload formats
  6. Sample IDs are alphanumeric
  7. Metadata rows in correct order: Class → Batch → Order

Despite all of the above, the error persists across all batch correction methods (automatic, EigenMS, ComBat, etc.). Most importantly, a data file that successfully underwent batch correction in this module last week is now returning the same “not eligible” error with no changes to the file. Is it possible that the batch correction module is currently experiencing a server-wide issue, rather than formatting problems causing the error? If so, when is the estimated timeline for resolving this issue?

Thank you so much for the help and guidance!

3 Likes
Volcano plot visualization and batch effect correction not working
2

But what is your input? The post you refer to also asked the same question.

3

BC_input_1.csv (225.5 KB)

Hello @xia.lab

I am a collaborator of jd omics. Attached is a merged file with samples in rows that previously was accepted in the batch correction module. It now returns the aforementioned error message. Your assistance is greatly appreciated!

Best,

AV

4

Hello xia.lab,

I am doing a batch correction using QC-RLSC but I get this error message:

I have 4 QC samples (2 QC samples for 2 batches).

When I used COMBAT, the batch correction module is running.

Can you explain why COMBAT works but not QC-RLSC please?

Thanks for your help

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image312×100 7.07 KB

5

Hello,

Sharing an update: The Batch Correction Module now works for my formatted data. Thank you so much to the Xia.Lab team for their help and input!