Difference between revisions of "Using Bioconductor To Analyse Microarray Data"
From Bridges Lab Protocols
Davebridges (Talk | contribs) m (→Obtaining GEO Datasets) |
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library(GEOquery) | library(GEOquery) | ||
</pre> | </pre> | ||
| − | * | + | *Can load: |
**datasets - '''GDS''' | **datasets - '''GDS''' | ||
**measurements - '''GSM''' | **measurements - '''GSM''' | ||
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gds <- getGEO("GDS162") #load GDS162 dataset | gds <- getGEO("GDS162") #load GDS162 dataset | ||
</pre> | </pre> | ||
| + | *see [[http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/r/geo/]] or [[http://www.bioconductor.org/packages/1.8/bioc/html/GEOquery.html]] for more information | ||
Revision as of 23:54, 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)
- Can load:
- datasets - GDS
- measurements - GSM
- platforms - GPL
- series - GSE)
gds <- getGEO("GDS162") #load GDS162 dataset
