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EDePasquale / DoubletDecon

A tool for removing doublets from single-cell RNA-seq data
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Error in (function (side, at = NULL, labels = TRUE, tick = TRUE, line = NA, : no locations are finite #31

Open DirtyHarry80 opened 4 years ago

DirtyHarry80 commented 4 years ago

I got this error while executing Main_Doublet_Decon function with a particular Seurat Object. Changing the Seurat Object (another dataset) removed the error. Any clues? This is how I proceeded from the Seurat object:

new.file=Improved_Seurat_Pre_Process(Seuratobj, num_genes=50, write_files=FALSE)

filename="newFile" location="/Volumes/Samsung_T5/" write.table(new.file$newExpressionFile, paste0(location=location, filename=filename, "_expression"), sep="\t") write.table(new.file$newFullExpressionFile, paste0(location=location, filename=filename, "_fullExpression"), sep="\t") write.table(new.file$newGroupsFile, paste0(location=location, filename=filename, "_groups"), sep="\t", col.names = F)

res.new.file=Main_Doublet_Decon(rawDataFile=new.file$newExpressionFile, groupsFile=new.file$newGroupsFile, filename=filename, location=location, fullDataFile=NULL, removeCC=FALSE, species="hsa", rhop=1.1, write=TRUE, PMF=TRUE, useFull=FALSE, heatmap=FALSE, centroids=TRUE, num_doubs=100, only50=FALSE, min_uniq=4, nCores=-1)

EDePasquale commented 4 years ago

Hi Andrei,

I think the three links I provided on the previous response to you would answer this question. If it doesn't, just ping me again and I can elaborate.

Best, Erica