Marcel Schilling

@jberkenbilt: Have you considered crowdsourcing such costs? If you let people know why you had to spend this and that money for the sake of improving qpdf, I'd be surprised...

It gets even weirder: ```r nrow(sobj) ``` ``` 12572 ```` ```r nrow(GetAssayData(sobj)) ``` ``` 12572 ``` ```r subset(sobj, features=rownames(GetAssayData(sobj))) ``` ``` An object of class Seurat 25144 features across 2700...

```r DefaultAssay(sobj)

@satijalab, @mojaveazure: I just noticed I posted this on the `seurat-data` repo. Would you mind [transferring](https://docs.github.com/en/issues/tracking-your-work-with-issues/transferring-an-issue-to-another-repository) it over to `seurat`, so I don't need to close it here and re-open...

cc @Alexis-Varin, as you had some helpful insights for [a similar issue](https://github.com/satijalab/seurat/issues/8750).

```r subset(sobj, features=head(rownames(sobj[["SCT"]]$data))) ``` ``` Error in .subscript.2ary(x, i, j, drop = TRUE) : subscript out of bounds ``` ```r subset(sobj, features=head(rownames(sobj[["SCT"]]$counts))) ``` ``` Error in .subscript.2ary(x, i, j, drop...

Is there anything I can do to track this down? Is SCT simply not supported/maintained/tested in Seurat anymore? If so, maybe [the corresponding vignette](https://satijalab.org/seurat/articles/sctransform_vignette) should be updated/archived to reflect that...

In case it helps: I tracked it down to [this line](https://github.com/satijalab/seurat-object/blob/ccc19843613382623fafacd21b459ad5bd21f593/R/seurat.R#L3569), which passes when `assay` is `"RNA"` but fails when it is `"SCT"` for the example data above. --- *update*:...

Here is how far I got: `subset.Seurat(features = ...)` starts by subsetting the Assay data and then updates the `n.counts` via `CalcN` which uses the `LayerData` of the (subset!) `SCT`...

I can confirm that modifying `CaclN` to pass the `layer` parameter to override the `'counts'` default value 'fixes' this issue. However, I have no clue if it results in the...