[Bioc-devel] Updates to SingleCellExperiment class structure - no action required

[Kasper Daniel Hansen]

It sounds to me that the class definition / structure is updated. You
should also have an associated updateObject() method to deal with this;
that's tradition. Of course, you may already have addressed this and just
not written about it in your email.

On Sun, Feb 16, 2020 at 3:51 AM Aaron Lun <
infinite.monkeys.with.keyboards using gmail.com> wrote:

> 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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>


-- 
Best,
Kasper

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