Using Bioconductor To Analyse Microarray Data

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

• see [Peter Cock's Page] or [GEOquery Documentation] for more information.