Want to explore gcPCA?
I have prepared a detailed tutorial to help you get started:
github.com/SjulsonLab/generalized_contrastive_PCA/tree/main/tutorial
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So we developed gcPCA, a flexible approach that builds on the strengths of cPCA while addressing its limitations.
The key idea?
We add a normalization in the objective function to identify dimensions with the largest relative change in variance between conditions.
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But it’s not as simple as just “removing” the hyperparameter. In real-world biological data, especially when sample sizes are small, random fluctuations in high-variance dimensions can overshadow the true signal.
We believe cPCA introduced the α to try to suppress these fluctuations.
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That’s when the idea for generalized contrastive PCA (gcPCA) was born.
What if we could:
- Remove the hyperparameter α?
- Make the method symmetric, treating both datasets equally.
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We initially tried using contrastive PCA (cPCA), which showed promise. However, it came with a drawback:
- A hyperparameter (α) controls the comparison, and different (α) values give equally probable solutions.
- It uses one experimental condition as a control, creating asymmetric comparisons.
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Our team works with high-dimensional datasets, think large-scale electrophysiology, single-cell RNA-seq, etc. In our last project, we hit a wall: how do you compare two experimental conditions (e.g., asleep vs. awake neural activity) when existing tools focus on one dataset at a time?
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Does your research involve comparing experimental conditions? Then our latest publication is for you: We developed generalized contrastive PCA (gcPCA), a tool for comparing high-dimensional datasets. 🧠📊 doi.org/10.1371/journal.pcbi.1012747
This tool was born out of necessity, here is the story. 🧵
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Doom running on a PDF made my day

github.com/ading2210/do...