Using Bioconductor To Analyse Microarray Data

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Software Requirements

  • R, get from [CRAN]
  • Bioconductor, get from [Bioconductor]
  • Bioconductor packages. Install as needed:
    • Biobase
    • GEOquery
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
  • see [[1]] or [[2]] for more information
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