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<<setup, include=FALSE, cache=FALSE>>=
library(knitr)
# set global chunk options
opts_chunk$set(fig.path='figure/minimal-', fig.align='center', fig.show='hold')
options(replace.assign=TRUE,width=90)
@

\title{Knitr example with an RNA Degradation Model}
\author{Todd R. Riley}
\maketitle

First, we must load the affy and ALLMLL packages, and then load the MLL.B dataset from the ALLMLL package:
<<results='hide', message=FALSE>>=
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: 
<<message=FALSE>>=
degrade <- AffyRNAdeg(MLL.B)
plotAffyRNAdeg(degrade, col=1:20)
@


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

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