Using Bioconductor To Analyse Microarray Data: Difference between revisions

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library(GEOquery)
library(GEOquery)
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</pre>
*Load data (can load datasets - '''GDS''',measurements -'''GSM''', platforms - '''GPL''' or series - '''GSE''')
*Load data (can load:
**datasets - '''GDS'''
**measurements - '''GSM'''
**platforms - '''GPL'''
***series - '''GSE''')
<pre>
<pre>
gds <- getGEO("GDS162")  #load GDS162 dataset
gds <- getGEO("GDS162")  #load GDS162 dataset
</pre>
</pre>

Revision as of 23:52, 26 July 2009


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
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