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Load the affy data into the R environment using the following code.
### Load the appropriate library for reading affy data, and inspect the data.
library( 'affy' )
soy.ab <- ReadAffy( 'geo_data/GSM209576.CEL.gz',
'geo_data/GSM209585.CEL.gz',
'geo_data/GSM209594.CEL.gz',
'geo_data/GSM209577.CEL.gz',
'geo_data/GSM209586.CEL.gz',
'geo_data/GSM209595.CEL.gz',
## we have gz files which R can read in.
compress=TRUE)
## Inspect the loaded data. This will make a network connection first time
## around and can be slow.
soy.ab
## Check out the names of the samples.
sampleNames( soy.ab )
## as the current sample names refer to the original files, we change this for
## something more, er, easy to remember.
new.sampleNames <- c('hr.a3.12','hr.b3.12','hr.c3.12',
'ts.a4.12','ts.b4.12','ts.c4.12')
sampleNames(soy.ab) <- new.sampleNames
## and check that it has worked
sampleNames( soy.ab )
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