Using Bioconductor To Analyse Beadarray Data: Difference between revisions

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source("http://www.bioconductor.org/biocLite.R")
source("http://www.bioconductor.org/biocLite.R")
biocLite("PACKAGE")
biocLite("PACKAGE")
</pre>
==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 (Control Probe, normally a txt file)
<pre>
data = "FinalReport_SampleProbe.txt"
controls = "ControlProbe.txt"
samplesheet = "Proj_54_12Aug09_WGGEX_SS_name.csv"
BSData = readBeadSummaryData(dataFile = data, qcFile= controls, sampleSheet=samplesheet, controlID="TargetID")
</pre>
</pre>

Revision as of 17:21, 21 August 2009


Software Requirements

  • R, get from [CRAN]
  • Bioconductor, get from [Bioconductor]
  • Bioconductor packages. Install as needed:
    • beadarray
    • limma
source("http://www.bioconductor.org/biocLite.R")
biocLite("PACKAGE")

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 (Control Probe, normally a txt file)
data = "FinalReport_SampleProbe.txt"
controls = "ControlProbe.txt"
samplesheet = "Proj_54_12Aug09_WGGEX_SS_name.csv"
BSData = readBeadSummaryData(dataFile = data, qcFile= controls, sampleSheet=samplesheet, controlID="TargetID")
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