Bridges Lab Protocols

Using Bioconductor To Analyse Beadarray Data (lumi): Difference between revisions

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*At a minimum you need the Probe Profile data (normally a txt file).
*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.
*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 (Control Probe, normally a txt file)
*Load the beadarray library, indictate dataFile (required) and mapping library (shown here is mouse)
<pre>
<pre>
data = "FinalReport_SampleProbe.txt"
data = "FinalReport_SampleProbe.txt"
controls = "ControlProbe.txt"
lumi = lumiR(data, lib='lumiMouseIDMapping')
samplesheet = "Proj_54_12Aug09_WGGEX_SS_name.csv"
BSData = readBeadSummaryData(dataFile = data, qcFile= controls, sampleSheet=samplesheet)
</pre>
</pre>
*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 lumi.  Phenotype data can be accessed by pData(BSData) and expression data can be accessed by exprs(BSData).
*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).


==Data Normalisation==
==Data Normalisation==
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