Difference between revisions of "Using Bioconductor To Analyse Microarray Data"

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m (Obtaining GEO Datasets)
m (Obtaining GEO Datasets)
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<pre>
 
<pre>
 
gds <- getGEO("GDS162")  #load GDS162 dataset
 
gds <- getGEO("GDS162")  #load GDS162 dataset
 +
Meta(gds)  #show extracted meta data
 +
table(gds)[1:10,]  #show first ten rows of dataset
 
eset <- GDS2eset(gds)  #convert to expression set
 
eset <- GDS2eset(gds)  #convert to expression set
 
</pre>
 
</pre>
 
*see [[http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/r/geo/ Peter Cock's Page]] or [[http://www.bioconductor.org/packages/1.8/bioc/html/GEOquery.html GEOquery Documentation]] for more information.
 
*see [[http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/r/geo/ Peter Cock's Page]] or [[http://www.bioconductor.org/packages/1.8/bioc/html/GEOquery.html GEOquery Documentation]] for more information.

Revision as of 00:03, 27 July 2009


Software Requirements

  • R, get from [CRAN]
  • Bioconductor, get from [Bioconductor]
  • Bioconductor packages. Install as needed:
    • Biobase
    • GEOquery - [1]
source("http://www.bioconductor.org/biocLite.R")
biocLite("PACKAGE")

Obtaining GEO Datasets

  • Open a R terminal
  • Load Biobase and GEOquery packages
libary(Biobase)
library(GEOquery)
  • Can load:
    • datasets - GDS
    • measurements - GSM
    • platforms - GPL
    • series - GSE
gds <- getGEO("GDS162")  #load GDS162 dataset
Meta(gds)  #show extracted meta data
table(gds)[1:10,]  #show first ten rows of dataset
eset <- GDS2eset(gds)  #convert to expression set