Running quantiseq

[sjb-a11y]

any(duplicated(rownames(exprs_matrix)))
[1] FALSE
res = deconvolute(exprs_matrix, "quantiseq")

Running quantiseq

Running quanTIseq deconvolution module

Gene expression normalization and re-annotation (arrays: FALSE)

Warning: non-unique value when setting 'row.names': ‘entry withdrawn’
Error in .rowNamesDF<-(x, value = value) : 不允许有重复的'row.names'

[joan-yanqiong]

Hi,

I had the exact same problem, I just tried installing "omnideconv/[email protected]", this seems to work for me. Not sure how that impacts the other tools though.

[mlist]

Could you please provide a minimal example of reproducing this error?

[joan-yanqiong]

Hi, I just moved on and just installed "omnideconv/[email protected]", so I do not have a full reproducible example.

But I was using this code snippet essentially:

 tpm_quantiseq <- tpm
    rownames(tpm_quantiseq) <- toupper(rownames(tpm_quantiseq))
    cell_fractions <- immunedeconv::deconvolute(tpm_quantiseq, "quantiseq", tumor = TRUE, arrays = FALSE, scale_mrna = TRUE) %>% column_to_rownames("cell_type")