user2846211 - 4 months ago 31

R Question

I have a 132 x 107 dataset which consists of 2 patient types - (33 of patient 1) and (99 of patient 2).

I'm looking for outliers so I've run pca on the dataset and done qqplots of the 1st 4 components, using the following commands

`pca = prcomp(data, scale. = TRUE)`

plot(pca$x, pch = 20, col = c(rep("red", 33), rep("blue", 99)))

When I do the qqplot of the 2nd component using:

`qqPlot(pca$x[,2],pch = 20, col = c(rep("red", 33), rep("blue", 99)))`

the following graph shows 2 clear outliers - the red dots in the bottom left corner which are patient 1s.

Is there any straightforward way of working out the index of these points in the data so they can be removed?

Answer

For some reason, I don't believe that the identify method is supported
in the `car`

package (the source of `qqPlot()`

)

Let's take a look at a PCA of the USArrests data...

```
pca <- prcomp(USArrests)
```

The plot of this using `qqPlot`

is easy enough.

```
require(car)
qqPlot(pca$x[,2],pch = 20, col = c(rep("red", 33), rep("blue", 99)))
```

However, `qqPlot()`

does not allow for point selection via `identify()`

.

```
identify(qqPlot(pca$x[,2],pch = 20, col = c(rep("red", 33), rep("blue", 99))))
# numeric(0)
```

You can, however, make use of `qqnorm()`

in the `stats`

package.

```
identify(qqnorm(pca$x[,2],pch = 20, col = c(rep("red", 33), rep("blue", 99))))
```

This will produce a less sophisticated graph, but you should be able to add a line and confidence intervals manually via `qqline()`

(also in `stats`

) and a little more math.