Home

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

ChipEffectSet as ExpressionSet

NOTE (July 9, 2011): In order to use extractExpressionSet(), the latest patches need to be installed;

  source("http://aroma-project.org/hbLite.R");
  hbInstall("aroma.affymetrix");

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);
> 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);
> 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"