Problem with removeCC - Githubissues

EDePasquale / DoubletDecon

A tool for removing doublets from single-cell RNA-seq data

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Problem with removeCC #48

Open abigailelliot26 opened 3 years ago

abigailelliot26 commented 3 years ago

Based upon previous exploration of the data, I suspect that some cells with high cell cycle related gene expression are being called as doublets (likely because I have 2 or 3 different clusters that are high in cell cycle genes). But when I set removeCC = TRUE I get the following error:

Error in if (IDtype > 0) { : argument is of length zero

my species is danio rerio

EDePasquale commented 3 years ago

Hi,

My first thought was that I didn't include this species in my internal tables, but it does look like I have it there:

SpeciesName KEGGID SpeciesAbbr NCBIID Danio rerio. T01004 dre 7955

May I ask what species identifier you are using as the 'species' parameter?

Best, Erica

abigailelliot26 commented 3 years ago

Aha, sorry, I didn't have "Danio" capitalised - it works now!