Open MingyuYang-Yale opened 3 weeks ago
Hi Mingyu,
Have you successfully obtained the SVGs gene list? There should be the SVG stored in this variable: SVGs_infer_sig$gene.
And, can you check the spatial coordinates in the seurat obj? I'm not sure the coordinates are missing or not in your data. head(NA_merFISH_iSpatial@images$image@coordinates)
Thank you for your prompt reply!
I was able to successfully obtain the SVGs gene list. However, I noticed that the spatial coordinates in my Seurat object are slightly different, as they are not integers.
Additionally, when I ran the previous 'iSpatial::spatial_variable_genes' step, I received the following message: "As of Seurat v5, we recommend using AggregateExpression to perform pseudo-bulk analysis. The first group.by variable xy starts with a number, so we are appending g to ensure valid variable names." I'm not sure if this is causing the error.
Hi,
I'm trying to run the tutorial on the striatum dataset but I got this error message:
Could you please provide guidance on how to resolve this issue?
Thank you!
Mingyu