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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