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") | ||
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<pre> | <pre> | ||
gds <- getGEO("GDS162") #load GDS162 dataset | gds <- getGEO("GDS162") #load GDS162 dataset | ||
| + | eset <- GDS2eset(gds) #convert to expression set | ||
</pre> | </pre> | ||
| − | *see | + | *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 23:58, 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
eset <- GDS2eset(gds) #convert to expression set
