convert a seurat object to expressionset

Question

[Bine]

Dear all,

Could anyone advice me on how to convert a Seurat object to an ExpressionSet? Unfortunately I need this format for a specific analysis.

Thank you!

[bk11]

You are probably looking to do like this?

library(Seurat)    
ExpressionSet.SO = ExpressionSet(assayData = as.matrix(GetAssayData(SeuratObject)))

[Bine]

Thank you very much. Thats exactly what I am looking for.

The only thing I am missing this way is that it doesnt store my metadata from the Seurat object (subtype) in the phenotype data:

For me it looks like this now:

ExpressionSet (storageMode: lockedEnvironment)
assayData: 18373 features, 4697 samples 
element names: exprs 
protocolData: none
phenoData: none
featureData: none
experimentData: use 'experimentData(object)'

I would like it to look like this:

  ExpressionSet (storageMode: lockedEnvironment)
  assayData: 18373 features, 4697 samples 
  element names: exprs 
  protocolData: none
  phenoData
  rowNames: TCGA.02.0003.01A.01 TCGA.02.0010.01A.01 ...
  TCGA.12.0620.01A.01 (173 total)
  varLabels: subtype
  varMetadata: labelDescription channel
  featureData: none
  experimentData: use 'experimentData(object)'

Thanks a lot!