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re SingleCellExperiment and ExpressionSet #2

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haircell opened this issue Jan 5, 2019 · 1 comment
Open

re SingleCellExperiment and ExpressionSet #2

haircell opened this issue Jan 5, 2019 · 1 comment

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@haircell
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haircell commented Jan 5, 2019

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
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haowulab commented Jan 7, 2019

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.

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@haowulab @haircell