AvgExpression deprecation

[domjacri]

We will not fix until it is truly deprecated.

https://github.com/neurogenetics/SAHA/blob/main/R/Seurat2SAHA.R

[domjacri]

Ok, not fully deprecated however, layer has replaced slot in average expression. Need to fix sometime soon.

[richardmustaklem]

As of Jan 2026, Suerat2SAHA still works

[domjacri]

Note from @mmesecar that the AverageExpression deprecation warning is still popping up. Glad that it works as we designed but I want to silence it as not to confuse users. The AggregateExpression alternative may be recommended by Seurat for other functions, but it is not compatible with SAHA without further processing.

We decided to silence it in the "AvgExp" and "Both" for loops.

[richardmustaklem]

Updated. Please close once confirmed