Sam Morabito

icon indicating a website link https://smorabit.github.io/

icon company @Single-Cell-Genomics-Group-CNAG-CRG icon location Barcelona, Catalunya icon location Computational Biology Postdoctoral Researcher

Results 88 comments of Sam Morabito

undefined arguments in blockwiseConsensusModules

These parameters have been fixed in the newest version of hdWGCNA.

Error in checkSets(MEs, checkStructure = TRUE, useSets = useSets) : No data given.

Hi, thank you for taking the time to write this issue. I am wondering if you can distill this error into a simple example, ideally with the tutorial dataset, rather...

`ConstructMetaspots` not compatible with Seurat's `VisiumV2` class

Thank you for taking the time for writing this issue and for diagnosing the problem regarding the new class structure. FYI, I am currently very busy with some upcoming deadlines...

`ConstructMetaspots` not compatible with Seurat's `VisiumV2` class

This issue is not fully solved, it looks like the Visium V2 Seurat no longer uploads all the coordinates that are output from spaceranger, which ultimately causes issues with hdWGCNA....

ConstructNetwork() and ModuleEigengenes() functions use different methods to calculate the ME (module eigengene), leading to the discrepancy in the kME result

Hi, I think I understand your confusion. If you were following the tutorial, the network is constructed on a metacell representation of your dataset, which gives us a different gene...

ConstructNetwork() and ModuleEigengenes() functions use different methods to calculate the ME (module eigengene), leading to the discrepancy in the kME result

Currently there is not a way to do this directly with hdWGCNA but you might be able to write some custom code to do this if you want to.

`ConstructMetaspots`: `seurat_obj` not found

Thank you for pointing this out, just fixed it so please re-install hdWGCNA.

MetaspotsByGroups ERROR: invalid class “Assay5” object: Layers must be two-dimensional objects

The variables that you include in `group.by` should be categorical variables, not continuous. I am guessing that distance is a continuous variable, so in this case you should not use...

Error when running "ModuleEigengenes()" with a seurat.v5 object

Hi, I am unfortunately not able to reproduce your error. Is this problem specific to your dataset, or does it happen on any dataset that you use like the tutorial...

Error when running "ModuleEigengenes()" with a seurat.v5 object

Okay that is interesting, I have tested hdWGCNA successfully with Seurat v4 and Seurat v5 objects, but I have not tried using `UpdateSeuratObject`, so maybe the issue is related to...