Difference between revisions of "Using Bioconductor To Analyse Microarray Data"
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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
