PCA miscolored and groups mislabed

Hello developers,

I have an issue with PCA grafics.

These are the steps I follow.

Statistical Analysis [one factor]

  1. Upload the data: peak intensities, samples in rows (unpaired). The data is a csv file (attached).
  2. Missing values: STEP 1: remove with > 65% mvs. STEP 2: KNN(feature-wise).
  3. Filtering features: RSDs > 30%. Percentage to filter out: 0 %
  4. Normalization: none. Data transformation: log. Data scaling: autoscaling.
  5. PCA analysis > 2D Scores Plot: Look that QCs are the blue circles and the Severe group are the light green circles.
  6. Go to Data Editor > Edit Groups: remove the QC group.
  7. Apply the same normalization, transformation and scaling as did above (step 4).
  8. PCA analysis (in fact, no matters what analysis is selected in this step, should be PLS-DA also).
  9. Go back to Data Editor > Edit Groups: include the QC group.
  10. Same settings for normalization, transformation and scaling.
  11. PCA analysis > 2D Scores Plot: Look at QC and Severe groups. QC and Severe groups were interchanged. The blue circles correspond to samples of the severe group.

I add some screenshots:

PCA (step 5)

PCA (step 11)

As you can see, labels and colors were interchanged.

Thanks for the help.

Here the data: Input_MetabAnaly_E3.csv (188.1 KB)