Difference between revisions of "Using Bioconductor To Analyse Microarray Data"
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Meta(gds) #show extracted meta data | Meta(gds) #show extracted meta data | ||
table(gds)[1:10,] #show first ten rows of dataset | table(gds)[1:10,] #show first ten rows of dataset | ||
| − | eset <- GDS2eSet(gds) #convert to expression set | + | eset <- GDS2eSet(gds) #convert to expression set, by default obtains annotation (GPL) data and no log transformation. |
| + | pData(eset) #phenotype data | ||
| + | sampleNames(eset) #sample names (GSM) | ||
</pre> | </pre> | ||
*see [[http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/r/geo/ Peter Cock's Page]] or [[http://www.bioconductor.org/packages/1.8/bioc/html/GEOquery.html GEOquery Documentation]] for more information. | *see [[http://www2.warwick.ac.uk/fac/sci/moac/currentstudents/peter_cock/r/geo/ Peter Cock's Page]] or [[http://www.bioconductor.org/packages/1.8/bioc/html/GEOquery.html GEOquery Documentation]] for more information. | ||
Revision as of 00:09, 27 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
Meta(gds) #show extracted meta data
table(gds)[1:10,] #show first ten rows of dataset
eset <- GDS2eSet(gds) #convert to expression set, by default obtains annotation (GPL) data and no log transformation.
pData(eset) #phenotype data
sampleNames(eset) #sample names (GSM)
- see [Peter Cock's Page] or [GEOquery Documentation] for more information.
