Lukas Weber

Rebasing `SpatialImage` classes on `Annotated` in PR #122 now enables storing this in `metadata`. To do: update `read10xVisium()` and add examples as discussed in PR #122 .

Yes, I can see this now, especially with this example, and now that we have only `spatialCoords` (and `spatialData` which was more complicated / not a numeric matrix is gone)....

Hi all, we discussed this again today, and wanted to check if anyone had any more feedback or ideas before we proceed on this one. We are thinking it would...

Yes, I think this makes sense, thanks for following up @HelenaLC !

Yes, `spatialData` has been removed for several cycles now, so this sounds good to me, i.e. removing the code and warning messages completely. I think the version bumps is ok...

Hi J.D., Sorry for the delay in responding. I tried out some examples today, and you are right, the `show_logFC` argument doesn't work when using method `diffcyt-DA-GLMM`. I traced this...

Hi @tammyyyx , yes I believe we made some updates that may have affected this. Are you using the latest versions of `diffcyt` and `CATALYST` from Bioconductor? (Bioconductor 3.11, `diffcyt`...

Hi, did the suggestions Helena provided in the CATALYST repository help? As Helena suggested, one idea would be to also try one of the other DA methods, e.g. `method_DA =...

Ok thanks, I just clicked request access for my gmail account in the google drive link.

Yes, I have access now. Tagging the other issue you opened in the CATALYST repo so we can keep the discussion connected: https://github.com/HelenaLC/CATALYST/issues/110