Difference between revisions of "Using Bioconductor To Analyse Microarray Data"
From Bridges Lab Protocols
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libary(Biobase) | libary(Biobase) | ||
library(GEOquery) | library(GEOquery) | ||
| + | </pre> | ||
| + | *Load data (can load datasets - '''GDS''',measurements -'''GSM''', platforms - '''GPL''' or series - '''GSE''') | ||
| + | <pre> | ||
| + | gds <- getGEO("GDS162") #load GDS162 dataset | ||
</pre> | </pre> | ||
Revision as of 23:51, 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 or series - GSE)
gds <- getGEO("GDS162") #load GDS162 dataset
