How to: Extract probe signals as an 'affy' AffyBatch object

Probe-level data can be exported as an AffyBatch object (defined in the affy package) by calling:

ab <- extractAffyBatch(csR)

where csR is an AffymetrixCelSet. Note that this will load all data in to memory.

Example: HG-U133_Plus_2

csR <- AffymetrixCelSet$byName("Affymetrix-HeartBrain", chipType="HG-U133_Plus_2")
print(csR)

## AffymetrixCelSet:  
## Name: Affymetrix-HeartBrain  
## Tags:  
## Path: rawData/Affymetrix-HeartBrain/HG-U133_Plus_2  
## Platform: Affymetrix  
## Chip type: HG-U133_Plus_2  
## Number of arrays: 6  
## Names: u1332plus_ivt_cerebellum_A, u1332plus_ivt_cerebellum_B,
## ..., u1332plus_ivt_heart_C  
## Time period: 2005-07-14 14:13:24 -- 2005-07-19 11:54:06  
## Total file size: 77.55MB  
## RAM: 0.01MB


ab <- extractAffyBatch(csR)
print(ab)

## AffyBatch object  
## size of arrays=1164x1164 features (9 kb)  
## cdf=HG-U133_Plus_2 (54675 affyids)  
## number of samples=6  
## number of genes=54675  
## annotation=hgu133plus2  
## notes=


print(objectSize(ab@assayData))

## [1] 113811880