Using Bioconductor To Analyse Microarray Data: Difference between revisions

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*Bioconductor packages.  Install as needed:
*Bioconductor packages.  Install as needed:
**Biobase
**Biobase
**GEOquery
**GEOquery - [[http://www.bioconductor.org/packages/1.8/bioc/html/GEOquery.html]]
<pre>
<pre>
source("http://www.bioconductor.org/biocLite.R")
source("http://www.bioconductor.org/biocLite.R")

Revision as of 23:55, 26 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
  • see [[2]] or [[3]] for more information
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