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

Aaron Lun |n||n|te@monkey@@w|th@keybo@rd@ @end|ng |rom gm@||@com
Sun Feb 16 19:50:24 CET 2020

That would be correct.

On 2/16/20 6:38 AM, Kasper Daniel Hansen wrote:
> 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 
> <mailto: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
>     _______________________________________________
>     Bioc-devel using r-project.org <mailto:Bioc-devel using r-project.org> mailing list
>     https://stat.ethz.ch/mailman/listinfo/bioc-devel
> -- 
> Best,
> Kasper

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