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hemberg-lab / SC3

A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
http://bioconductor.org/packages/SC3
GNU General Public License v3.0
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sc3_plot_de_genes duplicate row names #55

Closed koelling closed 6 years ago

koelling commented 6 years ago

Maybe I am doing something wrong, but for some values of k I am getting the following error when calling sc3_plot_de_genes:

Warning message:
“non-unique value when setting 'row.names': ‘Lilrb4a’”
Error in `row.names<-.data.frame`(`*tmp*`, value = value): duplicate 'row.names' are not allowed
Traceback:

1. sc3_plot_de_genes(sce_named, k = k)
2. sc3_plot_de_genes(sce_named, k = k)
3. `rownames<-`(`*tmp*`, value = names(de_genes))
4. `row.names<-`(`*tmp*`, value = value)
5. `row.names<-.data.frame`(`*tmp*`, value = value)
6. stop("duplicate 'row.names' are not allowed")

Is it possible that there is a bug somewhere, maybe if a gene is called as differentially expressed for multiple clusters somehow?

koelling commented 6 years ago

I'm using SC3_1.7.6

wikiselev commented 6 years ago

@koelling sorry for a delayed response, have you figured the problem? If not, could you please share your dataset with vk6@sanger.ac.uk?