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</pre>
*You may need to alter either the ProbeID or ControlID to fit the illuminaprobe column from the sampleprobe or controlprobe datasets.
==Data Normalisation==
*Microarray data is typically quantile normalised and log2 transformed:
<pre>BSData.quantile = normaliseIllumina(BSData, method="quantile", transform="log2")</pre>
*To examine the effects of normalisation on the dataset use boxplots:
<pre>
boxplot(as.data.frame(log2(exprs(BSData))),las=2,outline=FALSE, ylab="Intensity (Log2 Scale)")
boxplot(as.data.frame(exprs(BSData.quantile)),las=2,outline=FALSE, ylab="Intensity (Log2 Scale)")
</pre>
*Save these boxplots as postscript files.
*This fits the data into the BSData dataframe. Phenotype data can be accessed by pData(BSData) and expression data can be accessed by exprs(BSData).