I have an issue with PCA grafics.
These are the steps I follow.
Statistical Analysis [one factor]
- Upload the data: peak intensities, samples in rows (unpaired). The data is a csv file (attached).
- Missing values: STEP 1: remove with > 65% mvs. STEP 2: KNN(feature-wise).
- Filtering features: RSDs > 30%. Percentage to filter out: 0 %
- Normalization: none. Data transformation: log. Data scaling: autoscaling.
- PCA analysis > 2D Scores Plot: Look that QCs are the blue circles and the Severe group are the light green circles.
- Go to Data Editor > Edit Groups: remove the QC group.
- Apply the same normalization, transformation and scaling as did above (step 4).
- PCA analysis (in fact, no matters what analysis is selected in this step, should be PLS-DA also).
- Go back to Data Editor > Edit Groups: include the QC group.
- Same settings for normalization, transformation and scaling.
- 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)