Incorrect VST normalization

[bolak92]

Describe the bug

While attempting to run VST (Variance Stabilizing Transformation) normalization using AlphaPept, I encountered several issues that suggest the normalization process might not be functioning as intended.

Issue 1: Axis of Normalization Upon debugging, it appears that the normalization is being performed across proteins (columns in ds.mat) rather than across samples (rows). Below is a screenshot of a table that supports my hypothesis:

To Reproduce: I used a standard ProteinGroups.txt file and preprocessed it using the following code:

ds.preprocess(
    remove_contaminations=True,
    normalization = "vst"
)

Issue 2: Inconsistent PCA Graphs The PCA graphs generated post-normalization are inconsistent, both in terms of axis scales and explained variance. Here's a screenshot for reference:

Issue 3: VST vs VSN Normalization Is the VST normalization in AlphaPept intended to perform similarly to the VSN normalization method available in R? For reference, here is the VSN documentation.

Additional Information Operating System: Windows 10 Python Environment: Conda

I would appreciate any guidance or fixes for these issues. Thank you!