Is the ExpressionSet Class Deprecated?
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cannin ▴ 20
@cannin-6903
Last seen 1 day ago
United States

Is the ExpressionSet class deprecated? If it is, what are the ramifications of this?

• Are new packages barred from using ExpressionSet?
• Will existing packages that use ExpressionSet be forced to move to SummarizedExperiment? If so, when?
• Often deprecation means the removal of support. If ExpressionSet is deprecated will support be removed? If so, when?
• Is SummarizedExperiment the replacement? Is SummarizedExperiment a superset of ExpressionSet with all ExpressionSet features available?
expressionset • 308 views
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@james-w-macdonald-5106
Last seen 1 day ago
United States

Why do you think the ExpressionSet class is deprecated? Trying to deprecate a foundational class like that would cause some pretty extensive breakage for any number of packages, and I can't imagine what the upside would be. The cost of deprecating would be far higher than the cost to just keep it around, so I can't imagine it will ever go away. I mean, I've tried like 3-4 times to convince people that the affy package should go away and never got any traction, and that package isn't nearly as entrenched as the ExpressionSet is.

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@martin-morgan-1513
Last seen 3 months ago
United States

But for new packages, especially those in the sequencing domain, SummarizedExperiment is a much better choice. It is better engineere, more flexible, and has more than 1200 'reverse dependencies' for interoperability.

If you submit a package in the sequencing domain, and it uses ExpressionSet, you'll be asked to support SummarizedExperiment (or SingleCellExperiment, or...) instead.