How to: Extract probeset summaries (chip effects) as a 'Biobase' eSet object

ChipEffectSet as eSet*

2010-02-08: The extractESet() method is not yet available.

Chip effects can be exported as an eSet object (defined in the Biobase package) by calling:

es <- extractESet(ces)

The extracted object will be annotated with as much information as possible at the time of the call. Note that this will load all data in to memory.

Example

ces <- getChipEffectSet(plm)
ces

## ChipEffectSet:
## Name: Affymetrix-HeartBrain
## Tags: RBC,QN,RMA
## Path: plmData/Affymetrix-HeartBrain,RBC,QN,RMA/HG-U133_Plus_2
## Platform: Affymetrix
## Chip type: HG-U133_Plus_2,monocell
## Number of arrays: 3
## Names: cerebellum_A, cerebellum_B, cerebellum_C
## Time period: 2009-08-12 22:21:58 -- 2009-08-12 22:21:59
## Total file size: 1.73MB
## RAM: 0.01MB
## Parameters: (probeModel: chr "pm")

es <- extractESet(ces)
es

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