915
edits
Changes
m
controls lumi = "ControlProbe.txt"samplesheet = "Proj_54_12Aug09_WGGEX_SS_name.csv"BSData = readBeadSummaryDatalumiR(dataFile = data, qcFile= controls, sampleSheetlib=samplesheet'lumiMouseIDMapping')
*You may need to alter either the ProbeID or ControlID to fit the illuminaprobe column from the sampleprobe or controlprobe datasets.*This fits the data into the BSData dataframelumi. Phenotype data can be accessed by pData(BSData) and expression data can be accessed by exprs(BSData).
→Loading Data
*At a minimum you need the Probe Profile data (normally a txt file).
*For all R procedures first change directory to your working directory then next create a new script, and save all executed lines in that script file.
*Load the beadarray library, indictate dataFile (required), sampleSheet (normally a xls or csv file) and control set mapping library (Control Probe, normally a txt fileshown here is mouse)
<pre>
data = "FinalReport_SampleProbe.txt"
</pre>
==Data Normalisation==