Dear list,
As of version 1.9.2, the SingleCellExperiment class structure has been
updated so that "sizeFactors()<-" will store values in a "sizeFactor"
field in the "colData()", rather than the internal metadata. This aims
to improve interoperability of the SCE size factors with functions that
retrieve information from the column metadata; see GitHub for details.
This change occurs under the hood in the "sizeFactors()" getter and
setter functions, so no action should be required from users who were
already using those functions to manipulate the SCE size factors.
Nonetheless, downstream developers should keep an eye on their unit
tests as some of the more fragile checks may fail, e.g., if they
hard-coded the expected column names of the "colData" of an SCE.
Version 1.9.2. also removes a bunch of deprecated functionality from the
package, which may cause unrelated failures; though this was pretty
esoteric stuff that didn't see a lot of use in the first place.
Best,
-A
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