problem with running CalculatePWProfiles

[nmalwinka]

Hi, I am trying to run Tempora on my dataset. I downloaded the right .gmt file(s) for mouse but keep getting error when running CalculatePWProfiles:

Calculating cluster average gene expression profile...Error in exprMatrix_bycluster[[i]] <- rowMeans(exprMatrix[, which(colnames(exprMatrix) %in% : attempt to select less than one element in integerOneIndex

is there any obvious thing i missed? I definitely have genes from the GO table in the rownames of my tempora_object data slot.

Thanks

[thinh-tran]

Hi! Sorry for the delayed response. I think Tempora might be throwing this error because it couldn't extract what clusters the cells belong to from meta.data. Can you check if the rownames of your gene expression matrix and the column names of your metadata dataframe are the same? If they're not the same, making sure they're similar and re-creating the tempora object should fix this error. If it doesn't, please let me know!

I have adjusted the CreateTemporaObject function to also check for cell names in both the expression matrix and the meta.data.

[nmalwinka]

Somehow the problem was to run the gsva, when i used method="ssgsea", it worked (??)

[piloter2]

I've met similar problems. I also expect your reply.

cortex_tempora <- CalculatePWProfiles(cortex_tempora, gmt_path = "Mouse_GO_AllPathways_no_GO_iea_December_11_2020_symbol.gmt", method="ssgsea", min.sz = 10, max.sz = 200, parallel.sz = 0)

Calculating cluster average gene expression profile...Error in GSEABase::getGmt(gmt_path) : all records in the GMT file must have >= 2 fields first invalid line: NA