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?

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.

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.