[Bioc-devel] New SE or new assay in SE?

[Laurent Gatto]

Dear all,

Assume we have a SummarizedExperiment object `se` that contains raw count data, and a method `doProcess` that processes the data to produce a matrix of identical dimensions (for example log-transformation, normalisation, imputation, ...). What are the opinions in favour or against the following two options

- `doProcess(se)` returns a new SE object 
- `doProcess(se)` adds a new assay to se

If you are interested about the broader context about this question, see https://github.com/waldronlab/MultiAssayExperiment/issues/266

Thank you in advance for your input.

Laurent