Troubleshooting SCTransform Error in Seurat: "Can't use NA as row index in a tibble for assignment"

Question

[Anisha]

Hello everyone,

I'm currently working on a single-cell RNA-seq analysis project focused on understanding the communication between cDCs and CD8+ T cells in melanoma, using Seurat in R. My goal is to integrate two datasets representing these cell types and to apply NicheNet analysis to uncover potential signaling pathways involved in their interaction within the tumor microenvironment.

After preprocessing my data, creating Seurat objects for each dataset, and attempting to normalize the data using SCTransform, I encountered the following error:

Error in `[<-`:
! Can't use NA as row index in a tibble for assignment.

Here are the key steps leading up to the error:

1. Loaded the data from two Excel files using readxl::read_excel and confirmed that the first row contains column names.
2. Created Seurat objects for each dataset using CreateSeuratObject.
3. Attempted to apply SCTransform to each Seurat object for normalization and encountered the error during this step.

I've checked for NA values in my metadata (there are none) and counts data, and ensured that the Seurat package and its dependencies are up to date. However, the issue persists.

Could anyone provide insights into what might be causing this error and how to resolve it? Any suggestions or alternative approaches for preprocessing and integrating these datasets would also be greatly appreciated.

Thank you in advance for your help!