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[[Category: R]]
[[Category: Bioinformatics]]
[[Category: Bioconductor]]
==Software Requirements==
*R, get from [[http://cran.r-project.org/ CRAN]]*Bioconductor, get from [[http://www.bioconductor.org/download Bioconductor]]
*Bioconductor packages. Install as needed:
**beadarray
**limma
**annotation data for the array (normally illuminaMousev2BeadID.db)
*To install bioconductor packages use:
<pre>
source("http://www.bioconductor.org/biocLite.R")
*First define groups for each treatment. If a samplesheet was provided correctly and had this information:
<pre>samples = pData(BSData)$Sample_Group</pre>
*Otherwise define these groups manually in the order that they were entered (, check by looking at pData(BSData)
<pre>samples = c("Control", "Control", "Treatment1", "Treatment1, "Treatment2"...)</pre>
*Next the groups are used to set up a statistical design:
data = cbind(anno,data)
write.csv = (data, file = "Filename.csv")
</pre>
*Remember that the expression set is Log2 adjusted, so to look at absolute expression levels use 2^value.