Difference between revisions of "Using Bioconductor To Analyse Beadarray Data"
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controls = "ControlProbe.txt" | controls = "ControlProbe.txt" | ||
samplesheet = "Proj_54_12Aug09_WGGEX_SS_name.csv" | samplesheet = "Proj_54_12Aug09_WGGEX_SS_name.csv" | ||
| − | BSData = readBeadSummaryData(dataFile = data, qcFile= controls, sampleSheet=samplesheet | + | 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 BSData dataframe. Phenotype data can be accessed by pData(BSData) and expression data can be accessed by exprs(BSData). | ||
Revision as of 17:23, 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)
- 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 dataframe. Phenotype data can be accessed by pData(BSData) and expression data can be accessed by exprs(BSData).
