R version 2.9.2 (2009-08-24)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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 - MKL libraries for acclerated math installed: see help (setMKLthreads)
 - ParallelR packages installed: see help (package='foreach')

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> png(filename="reading_and_investigating.r%02d.png")
> 
> ### 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
AffyBatch object
size of arrays=1164x1164 features (8 kb)
cdf=Soybean (61170 affyids)
number of samples=6
number of genes=61170
annotation=soybean
notes=  
> 
> ## Check out the names of the samples.
> sampleNames( soy.ab )
[1] "GSM209576.CEL.gz" "GSM209585.CEL.gz" "GSM209594.CEL.gz" "GSM209577.CEL.gz"
[5] "GSM209586.CEL.gz" "GSM209595.CEL.gz"
> 
> 
> 
> ## 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 )
[1] "hr.a3.12" "hr.b3.12" "hr.c3.12" "ts.a4.12" "ts.b4.12" "ts.c4.12"
> 
> 
> 
> warnings()
NULL
>