Dear Dr. Xia and MetaboAnalyst community,
I am using MetaboAnalyst (web version) for plant metabolomics analysis and have encountered an issue with the PCA module.
GC_test_clean.csv (28.0 KB)
The problem:
The 2D Scores Plot consistently fails to load, while the Scree Plot and the 3D Scores Plot from the same analysis are generated normally. The browser console shows repeated 404 errors, for example:
GET https://www.metaboanalyst.ca/MetaboAnalyst/resources/users/guest26405538.../pca_score2d_1_dpi150.png → 404 (Not Found)
This suggests the server fails to generate the image file for the 2D plot during my session, even though the PCA calculation itself runs correctly (the 3D plot relies on the same underlying scores).
Troubleshooting already done:
- Removed the 95% confidence ellipse
- Tested different PC combinations (PC1 vs PC2, PC1 vs PC3, PC2 vs PC3)
- Reprocessed the data from scratch, tested with multiple datasets
- Tested on different networks
- Cleared browser cache, tried different browsers, disabled extensions
Additional isolation test:
To rule out an account/session issue, I also ran the built-in example datasets provided by MetaboAnalyst, and the PCA 2D Scores Plot worked correctly for those.
As a workaround, I was able to generate the PCA 2D scores plot successfully using R directly with the same data, so the underlying data and calculation are valid — the issue seems isolated to the MetaboAnalyst web interface’s image generation step for the 2D plot specifically.
Attached:
A reduced version of my dataset (concentration table, metabolites in rows x 24 samples in columns, and 4 groups that reproduces the issue.
I’d really appreciate any guidance on what might be causing this, and I’m happy to provide any further details. Thank you for developing such a valuable tool for the metabolomics community.
Best regards,
Pedro Ivo
