Tagged Questions

0
votes
1answer
55 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 ...
0
votes
1answer
30 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, ...
0
votes
1answer
81 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 ...
4
votes
2answers
284 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 % ...
0
votes
1answer
181 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 ...
4
votes
1answer
1k 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 ...
5
votes
3answers
2k 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 ...
7
votes
5answers
261 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 ...
7
votes
3answers
632 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 ...
16
votes
3answers
935 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 ...
7
votes
2answers
8k views

Interpretation of biplots in principal components analysis in R

I am reviewing PCA concepts. I came across this nice tutorial - http://cran.r-project.org/web/packages/HSAUR/vignettes/Ch_principal_components_analysis.pdf on how to do PCA in R language. I don't ...
7
votes
2answers
889 views

Visualizing multiple “histograms”

I am having difficulties to select the right way to visualize data. Let's say we have bookstores that sells books, and every book has at least one category. For a bookstore, if we count all the ...