Linked Questions

7 votes
3 answers
1k views

Are there examples of more informative PCA plots? [duplicate]

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 explained)...
jermdemo's user avatar
  • 273
3 votes
0 answers
5k views

How to interpret ggbiplot() visualization of PCA in R? [duplicate]

To apply and visualize PCA in R often ggbiplot() is used. What is the meaning of this plot ? Why it is useful for PCA ? We can consider this example: https://tgmstat.wordpress.com/2013/11/28/...
Ef_Ci's user avatar
  • 131
0 votes
0 answers
70 views

Visualizing and interpreting principal components [duplicate]

I have performed principal component analysis (PCA) in Matlab via [U,S,V] = svd(X) Now I have to show the principal directions of the considered principal ...
Jamgreen's user avatar
  • 383
264 votes
15 answers
294k views

What are the differences between Factor Analysis and Principal Component Analysis?

It seems that a number of the statistical packages that I use wrap these two concepts together. However, I'm wondering if there are different assumptions or data 'formalities' that must be true to use ...
Brandon Bertelsen's user avatar
24 votes
1 answer
15k views

Positioning the arrows on a PCA biplot

I am looking to implement a biplot for principal component analysis (PCA) in JavaScript. My question is, how do I determine the coordinates of the arrows from the $U,V,D$ output of the singular vector ...
ktdrv's user avatar
  • 450
13 votes
1 answer
33k views

What is the difference between "loadings" and "correlation loadings" in PCA and PLS?

One common thing to do when doing Principal Component Analysis (PCA) is to plot two loadings against each other to investigate the relationships between the variables. In the paper accompanying the ...
user1593755's user avatar
12 votes
2 answers
40k views

Post-hoc tests for MANOVA: univariate ANOVAs or discriminant analysis?

I am using a MANOVA test to compare nine different dependent variables (from neuropsychological and neuropsychiatric assessment) between three groups. The output shows a significant influence from ...
TvBalkom's user avatar
  • 380
6 votes
1 answer
4k views

Eigenvalues of correlation matrices exhibit exponential decay

I have a data-set of $P$ samples of size $N$, and noticed that the eigenvalues of the correlation matrices $A^TA$, when presented in descending order, can in many cases be described as an exponential ...
Uri Cohen's user avatar
  • 427
4 votes
1 answer
10k 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 ...
Shafi's user avatar
  • 41
2 votes
1 answer
350 views

Pre-PCA pooling in R

I was just wondering if it is possible to pool the data into groups before doing prcomp() in R? I have i.e. 100 individuals (rows) and 50 measurements(cols) with individuals being grouped in separate ...
Fedja Blagojevic's user avatar