Hi Sean,

Do you know that eset generated from GDS dataset a few month ago is different from the eset generated now?

Old eset:

> eset
ExpressionSet (storageMode: lockedEnvironment)
assayData: 22690 features, 5 samples
  element names: exprs
protocolData: none
phenoData
  sampleNames: GSM60394 GSM60393 ... GSM60391 (5 total)
  varLabels: sample protocol disease.state description
  varMetadata: labelDescription
featureData
  featureNames: 1415670_at 1415671_at ... AFFX-TrpnX-M_at (22690 total)
  fvarLabels: ID Gene.title ... GO.Component.1 (21 total)
  fvarMetadata: Column labelDescription
experimentData: use 'experimentData(object)'
Annotation:


New eset:

> eset
ExpressionSet (storageMode: lockedEnvironment)
assayData: 22690 features, 5 samples
  element names: exprs
protocolData: none
phenoData
  sampleNames: GSM60394 GSM60393 ... GSM60391 (5 total)
  varLabels: sample protocol disease.state description
  varMetadata: labelDescription
featureData
  featureNames: 1415670_at 1415671_at ... AFFX-TrpnX-M_at (22690 total)
  fvarLabels: 1 2 ... 21 (21 total)
  fvarMetadata: Column labelDescription
experimentData: use 'experimentData(object)'
Annotation:

The difference is in  fvarLabels.

Could you advise? How to get these names back?

Jing

OHSU


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