Using Bioconductor To Analyse Microarray Data
From Bridges Lab Protocols
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
- see [Peter Cock's Page] or [GEOquery Documentation] for more information.
