Permutation test does not complete for PLS-DA analysis

[Joseline]

Hi,
It’s been months now that I’ve tried unsuccessfully to run a permutation test on PLS-DA. I would like to know if you guys have tried to fix the issue. Note: I used the web platform on Mac Safari, and Mac Chrome, different Macs computers, and got the same error.
After reviewing the Requirements for Troubleshooting, I decided to try one of the test data sets, and it didn’t work either. Here’s my path:

1. Statistical Analysis (one-factor) module
2. Try our test data: “Concentrations”; Metabolite concentrations of 39 rumen samples measured by proton NMR from dairy cows fed with different proportions of barley grain (Ametaj BN, et al.). Group label - 0, 15, 30, or 45 - indicating the percentage of grain in diet.
3. Proceed without performing group editing
4. Normalization: Tried a few models, finally selected Normalization = None, Data transformation = Log 10, Data Scaling = None.
5. ANOVA = p value 0.05
6. PCA = Display top 5 PCs
7. PLS-DA = Top 5 components
8. Permutation = by Separation Distance, 1000 permutation numbers, SUBMIT.

It looks like it does something but the image never downloads, when clicking on the color palette symbol to download the image, I get the message HTTP Status 404 - Not Found on a new tab. Attached is the screenshot. I used the test data for your convenience. Please advice. Thanks.

[jeff.xia]

Have you performed cross validation (CV)? In general, you need to first use CV to find the optimal number of components for the model (not the default 5), then use Permutation to validate the model.

We will add a mesage for this case

[Joseline]

Thank you for replying. No, I have not. I’ll do that and see. Thanks!

[Joseline]

All fixed!! Thank you so much for your response and guidance! You guys are the BEST!!