Using Bioconductor To Analyse Microarray Data

From Bridges Lab Protocols
Revision as of 23:53, 26 July 2009 by Davebridges (Talk | contribs) (→‎Obtaining GEO Datasets)

Jump to: navigation, search


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)
  • Load data (can load:
    • datasets - GDS
    • measurements - GSM
    • platforms - GPL
    • series - GSE)
gds <- getGEO("GDS162")  #load GDS162 dataset
Retrieved from "http://bridgeslab.sph.umich.edu/protocols/index.php?title=Using_Bioconductor_To_Analyse_Microarray_Data&oldid=235"