While reading about PCA, I came across the following explanation:

Suppose we have a data set where each data point represents a single student’s scores on a math test, a physics test, a reading comprehension test, and a vocabulary test.

We find the first two principal components, which capture 90% of the variability in the data, and interpret their loadings. We conclude

that the first principal component represents overall academic

ability, and the second represents a contrast between quantitative

ability and verbal ability.The text states that PC1 and PC2 loadings are $(0.5, 0.5, 0.5, 0.5)$ for PC1 and $(0.5, 0.5, -0.5, -0.5)$ for PC2, and offers the following explanation:

[T]he first component is proportional to average score, and the second component measures the difference between the first pair of scores and the second pair of scores.

I am not able to understand what this explanation means.

**Answer**

Loadings (which should not be confused with eigenvectors) have the following properties:

- Their sums of squares within each component are the eigenvalues

(components’ variances). - Loadings are coefficients in linear

combination predicting a variable by the (standardized) components.

You extracted 2 first PCs out of 4. Matrix of loadings $\bf A$ and the eigenvalues:

```
A (loadings)
PC1 PC2
X1 .5000000000 .5000000000
X2 .5000000000 .5000000000
X3 .5000000000 -.5000000000
X4 .5000000000 -.5000000000
Eigenvalues:
1.0000000000 1.0000000000
```

In this instance, both eigenvalues are equal. It is a rare case in real world, it says that PC1 and PC2 are of equal explanatory “strength”.

Suppose you also computed component values, `Nx2`

matrix $\bf C$, and you z-standardized (mean=0, st. dev.=1) them within each column. Then (as point 2 above says), $\bf \hat {X}=CA’$. But, because you left only 2 PCs out of 4 (you lack 2 more columns in $\bf A$) the restored data values $\bf \hat {X}$ are not exact, – there is an error (if eigenvalues 3, 4 are not zero).

OK. What are the coefficients to predict *components by variables*? Clearly, if $\bf A$ were full `4x4`

, these would be $\bf B=(A^{-1})’$. With non-square loading matrix, we may compute them as $\bf B= A \cdot diag(eigenvalues)^{-1}=(A^+)’$, where `diag(eigenvalues)`

is the square diagonal matrix with the eigenvalues on its diagonal, and `+`

superscript denotes pseudoinverse. In your case:

```
diag(eigenvalues):
1 0
0 1
B (coefficients to predict components by original variables):
PC1 PC2
X1 .5000000000 .5000000000
X2 .5000000000 .5000000000
X3 .5000000000 -.5000000000
X4 .5000000000 -.5000000000
```

So, if $\bf X$ is `Nx4`

matrix of original centered variables (or standardized variables, if you are doing PCA based on correlations rather than covariances), then $\bf C=XB$; $\bf C$ are standardized principal component scores. Which in your example is:

PC1 = 0.5*X1 + 0.5*X2 + 0.5*X3 + 0.5*X4 ~ (X1+X2+X3+X4)/4

“the first component is proportional to the average score”

PC2 = 0.5*X1 + 0.5*X2 – 0.5*X3 – 0.5*X4 = (0.5*X1 + 0.5*X2) – (0.5*X3 + 0.5*X4)

“the second component measures the difference between the first pair of scores and the second pair of scores”

In this example it appeared that $\bf B=A$, but in general case they are different.

*Note*: The above formula for the coefficients to compute component scores, $\bf B= A \cdot diag(eigenvalues)^{-1}$, is equivalent to $\bf B=R^{-1}A$, with $\bf R$ being the covariance (or correlation) matrix of variables. The latter formula comes directly from linear regression theory. The two formulas are equivalent within PCA context only. In factor analysis, they are not and to compute factor scores (which are always approximate in FA) one should rely on the second formula.

Related answers of mine:

More detailed about loadings vs eigenvectors.

How principal component scores and factor scores are computed.

**Attribution***Source : Link , Question Author : priyanka , Answer Author : Community*