Using Bioconductor To Analyse Microarray Data

From Bridges Lab Protocols
Revision as of 00:09, 27 July 2009 by Davebridges (Talk | contribs) (Obtaining GEO Datasets)

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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, by default obtains annotation (GPL) data and no log transformation.
pData(eset)  #phenotype data
sampleNames(eset)  #sample names (GSM)