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ShellyCoder / cellcall

inferring cell-cell communication from scRNA-seq of ligand-receptor
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A problem in scoring Ligand-receptor relation #24

Open ChintanBhavsar93 opened 2 years ago

ChintanBhavsar93 commented 2 years ago

Hi,

I am using cellcall for cell-cell communication in ovarian tumours. When I execute the code, I encounter the following error -

Warning messages: 1: In serialize(data, node$con) : 'package:stats' may not be available when loading 2: In min(logical(0), na.rm = FALSE) : no non-missing arguments to min; returning Inf 3: In max(logical(0), na.rm = FALSE) : no non-missing arguments to max; returning -Inf 4: In min(logical(0), na.rm = FALSE) : no non-missing arguments to min; returning Inf

Are these warning messages actually the reason for no interaction in my dataset? Any help would be appreciated!

RuoyangShao commented 2 years ago

Hi, I met the exactly same warnings and get ligand-receptor score matrices filled with 0. Have you figure out about this issue? Many thanks!

ChintanBhavsar93 commented 2 years ago

Hi @RuoyangShao, unfortunately, no. I haven't received or found any solution to this issue. Let me know if you have any luck. By the way, a quick question - are you working with RNA-seq data or protein data?

RuoyangShao commented 2 years ago

Hi @ChintanBhavsar93, I am working with scRNA-seq data and tried using the parameter method = "mean" and successfully got an non-zero output. Although whether this output works downstream is unknown, hope this could benefit your work!