Gregor Sturm

We moved from Rmd to quarto and started to split up the reports. Once https://github.com/nf-core/differentialabundance/pull/535 is merged, we can continue with this.

Fails for me with ``` Error: ! elements in `col` should be named vectors. Backtrace: ▆ 1. └─ComplexHeatmap::HeatmapAnnotation(...) 2. └─ComplexHeatmap:::stop_wrap("elements in `col` should be named vectors.") Quitting from 1403-0008_baseline_response_deseq2.parameterised.Rmd:870-929 [unnamed-chunk-20]...

Still getting the error. Probably something about the color palette for column annoation.

It works now 🎉 One problem in my example: one category (STUDYSITE) has way too many levels. I think for the heatmap annotations it would be useful to exclude columns...

In my example, the legend was still overlapping with the column annotations. I now moved the column annotations to the left.

Hi @Zhenghongc, in principle we are open to that. I assume you want to run this through the cellranger-multi aligner?

I think you still need to take the baseline level into account when building contrasts, as done here for DESeq2: https://github.com/nf-core/modules/blob/8846461fd688f29921c28dd4182913969a4f36c1/modules/nf-core/deseq2/differential/templates/deseq2_differential.R#L450-L457 DESeq2 allows to test contrasts with a `c(variable, target,...

So regarding the eBayes, it is necessary to call it after contrasts.fit, according to this example from the limma user guide: https://bioconductor.org/packages//2.11/bioc/vignettes/limma/inst/doc/usersguide.pdf It wouldn't be necessary to call it *before*...

ok, then here are my last two requests: - [ ] Can you please add a check that (variable, reference, target) contrasts are not combined with a custom formula? -...

I don't think the relevel or subset to contrast samples should work together with a custom contrast/formula. At the pipeline level, when specifying a formula and a contrast string, contrast...