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haowulab / SC2P

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re SingleCellExperiment and ExpressionSet #2

Open haircell opened 5 years ago

haircell commented 5 years ago

Hi, I'm interested in using this package for my scRNAseq data. Is it compatible with the SingleCellExperiment class? If so, how is this done please? (Is there a way to go from SCE to the ExpressionSet)? Thank you!

haowulab commented 5 years ago

It depends on what you have in SingleCellExperiment. Essentially for an ExpressionSet, you need a count matrix and AnnotatedDataFrame for cell information. You can extract those from a SingleCellExperiment object (using assays and colData functions), and then feed them into ExpressionSet.