Knitr example with an RNA Degradation Model
========================================================

**Todd R. Riley**

First, we must load the affy and ALLMLL packages, and then load the MLL.B dataset from the ALLMLL package:

```{r}
library(affy)
library(ALLMLL)
data(MLL.B, package = "ALLMLL")
```


The first line of the following R code will create an RNA degradation model. In the second line we will visualize the model with overlapping histogram plots: 

```{r}
degrade <- AffyRNAdeg(MLL.B)
```


```{r fig.width=7, fig.height=6}
plotAffyRNAdeg(degrade, col=1:20)
```


Number of probesets N in the RNA degradation calculations is `r degrade$N`. This plot shows the average degradation across all the probe locations in order 5' to 3'.