Usage question and luminal A bias?

[andrewdchen]

Hello!

I have some pseudobulked data (originally single cell counts) that I'm trying to feed through applySSP but I'm noticing that everything is being predicted as Luminal A. The code looks like the following:

gex_matrix <- brca_pb@assays$RNA$counts %>% as.matrix

all_genes_ssp_pam50 <- applySSP(gex=gex_matrix, id=rownames(gex_matrix), ssp.name="ssp.pam50")
all_genes_ssp_pam50 %>% table

I've tried using "ssp.subtype" and I've also tried converting gene ids between HGNC and ENSEMBL and it's still all luminal A. Wondering if I'm missing anything!

Thanks,