### 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 )