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dviraran / SingleR

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
GNU General Public License v3.0
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eror when creating custom reference #47

Open danshu opened 5 years ago

danshu commented 5 years ago

Hi,

Here is the error message: ref$de.genes = CreateVariableGeneSet(expr,types,200) Error in if (sum(A) == 1) { : missing value where TRUE/FALSE needed

Best, danshu

dviraran commented 5 years ago

try 

ref$de.genes = CreateVariableGeneSet(expr,as.character(types),200)

if this doesn't work, its still something related to 'types'.

danshu commented 5 years ago

Thanks! I found that this is caused by NA values in types.

A new error is: Error in rowsSd(ref) : could not find function "rowsSd" Which packages is needed for this function?

dviraran commented 5 years ago

Are you sure its rowsSd? I use the function rowSds, that comes from the package matrixStats. But, I don't think there is rowsSd in the code.

danshu commented 5 years ago

I'm just following this tutorial:http://comphealth.ucsf.edu/sample-apps/SingleR/SingleR_create.html Seems to be a typo on that page.

dviraran commented 5 years ago

Thanks, I'll fix it.