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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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Problem when try to use custom geneset reference #59

Open ChaDuss opened 5 years ago

ChaDuss commented 5 years ago

Hi, thanks for your great package, I have a problem when i try to CreateSinglerObject with a custom geneset, it gives me this message that i don't understand :

[1] "Dimensions of counts data: 20352x1843" [1] "Annotating data with ref..." [1] "Variable genes method: de" [1] "Number of DE genes:1440" [1] "Number of cells: 1843" [1] "Fine-tuning round on top cell types (using 1 CPU cores):" |======================================================================================================| 100%, Elapsed 00:27[1] "Number of DE genes:1440" [1] "Number of clusters: 20" [1] "Fine-tuning round on top cell types (using 1 CPU cores):" |======================================================================================================| 100%, Elapsed 00:00[1] "Annotating data with ref (Main types)..." Error in colnames<-(*tmp*, value = fgroups) : attempt to set 'colnames' on an object with less than two dimensions

Thanks for your help.

Charles

dviraran commented 5 years ago

Hi,

It seems that it is failing in the main types analysis. Did you define the main types fields? it is eventually just like defining the regular types but allows another (more broad) defintion for aggregating samples together. If you don't want to use that you can just use: do.main.types = F

ChaDuss commented 5 years ago

Thank you so much for your help now it works.

Charles