# Tagged Questions

117 views

### Interpretation of PCA biplot?

I just ran my first ever PCA, so please excuse any naivety on my part. As input, I used five years worth of the following: S&P/ASX 200 A-REIT S&P/ASX 200 Consumer Discretionary S&P/ASX ...
176 views

### Principal component analysis with Voxels (Vector Pixels) in Matlab

I have Vectors which have a certain position (Voxels) in an image. I would like to perform a pca to cluster out all Voxels which are correlating with each other. I have for example three Voxels in ...
615 views

### How to visualize what canonical correlation analysis does (in comparison to what principal component analysis does)?

Canonical correlation analysis (CCA) is a technique related to principal component analysis (PCA). While it is easy to teach PCA or linear regression using a scatter plot (see a few thousand examples ...
159 views

### How to project high dimensional space into a two-dimensional plane?

I have a set of data points in a N-dimensional space. In addition, I also have a centroid in this same N-dimensional space. Are there any approaches that can allow me to project these data points into ...
338 views

I am often disappointed with PCA plots in the scientific literature. Typically PCA plots do not provide a breakdown of the variables and their weights, just something like PCA1 (70% variance ...
85 views

### Plotting high dimensional data

I want to plot high dimensional data on x y plane. For that I know three methods: Principal component analysis (PCA), multidimensional scaling (MDS) and a method from spectral graph theory (using the ...
43 views

### What's the logic/motivation behind pre-filtering data based on variance?

I am currently working with gene expression data where I have a number of genes (variables) measured over a number of samples. I could not make sense of the statistics and visualization suite we have, ...
89 views

### Is a Biplot suitable ? Domestic Violence VS Non-Violence data

I have a small data set that consists solely of counts. I have several variables. For example State, for each state (Mexican States), for example, Tamauplipas I have the counts of domestic violence ...
424 views

### Appropriateness of PCA to visualize clusters in genetic data

I've seen PCA improperly applied in genetic research quite often. I wanted to clarify : when is it appropriate to use PCA as a visualization tool in your analysis? Some examples: 1) Rarely is the % ...
209 views

### Visualizing PCA time series

I have the following experiment. My predictors are: Plant area, 6 types of plants, 5 time points and 12 replicates for class. Time points are not equally spaced. A normal plot of Area vs. time will ...
2k views

### How to highlight predefined groups in PCA individual map?

This has a simple answer but it has been eluding me nonetheless. I have been trying to build a PCA plot from scratch with the ability to plot predefined groups in different colors. I can plot PCA ...
4k views

### Practical PCA tutorial with data

Searching the internet for PCA tutorial gives thousands of results (even videos). Many of the tutorials are very good. But I am not able to find any practical example where PCA is explained using some ...
341 views

### Dimensionality reduction technique to maximize separation of known clusters?

So let's say I have a bunch of data points in R^n, where n is pretty big (like, 50). I know this data falls into 3 clusters, and I know which cluster each data point is a part of. All I want to do is ...
671 views

### How to visualize the true dimensionality of the data?

I have a dataset that's nominally 16-dimensional. I have about 100 samples in one case and about 20,000 in another. Based on various exploratory analyses I've conducted using PCA and heat maps, I'm ...
1k views

### Visualizing a million, PCA edition

Is it possible to visualize the output of Principal Component Analysis in ways that give more insight than just summary tables? Is it possible to do it when the number of observations is large, say ...