Using numbat on multiple 10x visium spatial samples

[spatialbiology1]

Dear Teng Gao,

Thank you for developing a great tool. I am interested in applying 10x visium on matched primary and metastatic samples. Is there a way I can combine samples so that I can study global and unique CNV alterations between these samples?

Thanks
Zinn

[teng-gao]

Hi @spatialbiology1 ,

Multiple Visium (for fresh tissue) samples should work similarly as scRNA-seq samples. Please checkout this related issue
#111 and the spatial vignette.

Best,
Teng

[teng-gao]

Unfortunately Visium for FFPE is probe-based and it doesn't actually sequence the transcripts (so no SNP information is captured). Expression-only methods (InferCNV/CopyKAT) would be more suitable for these samples.