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

ChipEffectSet as ExpressionSet

Chip-effect sets can be exported as an ExpressionSet object (defined in the Biobase package) by calling:

eset <- extractExpressionSet(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)
print(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: 6
## Names: u1332plus_ivt_cerebellum_A, u1332plus_ivt_cerebellum_B, u1332plus_ivt_cerebellum_C, ..., u1332plus_ivt_heart_C [6]
## Time period: 2011-07-09 17:20:17 -- 2011-07-09 17:20:18
## Total file size: 3.45MB
## RAM: 0.01MB
## Parameters: (probeModel: chr "pm")

eset <- extractExpressionSet(ces)
print(eset)

## ExpressionSet (storageMode: lockedEnvironment)
## assayData: 54675 features, 6 samples
##   element names: exprs
## protocolData: none
## phenoData: none
## featureData: none
## experimentData: use 'experimentData(object)'
## Annotation:

sampleNames(eset)

## [1] "u1332plus_ivt_cerebellum_A" "u1332plus_ivt_cerebellum_B"
## [3] "u1332plus_ivt_cerebellum_C" "u1332plus_ivt_heart_A"
## [5] "u1332plus_ivt_heart_B"      "u1332plus_ivt_heart_C"

featureNames(eset)[101:110]
## [1] "200018_at"   "200019_s_at" "200020_at"   "200021_at"   "200022_at"
## [6] "200023_s_at" "200024_at"   "200025_s_at" "200026_at"   "200027_at"