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SCDC
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Error with SCDC_ENSEMBLE #28

Open ljarassier opened 2 years ago

ljarassier commented 2 years ago

Hi,

I have issue with the SCDC_ENSEMBLE command.

Result <- SCDC_ENSEMBLE(bulk.eset = bulkDataSet, sc.eset.list = scDataSetList, 
    ct.varname = "cellType", sample = "SubjectName", ct.sub = CTlist)

While running this command with one bulk and 3 scRNAseq, I got this error message : 

Error in if (sum(abs(prop.wt.new - prop.wt)) < epsilon) { :
  missing value where TRUE/FALSE needed

I kept only genes in all the datasets, CTlist contains the union of all the celltypes detected in the different scRNAseq datasets. Moreover, I performed SCDC_qc() command on all the scRNAseq datasets.

Is there something I do wrong ? Do you need more information ?

Thanks in advance for your help.

meichendong commented 2 years ago

Hi @ljarassier , sorry for the late response. According to your description, I think the error occurred because some scRNA-seq datasets do not have certain celltypes. The ENSEMBLE procedure is assuming that the major cell types of interest exist in all reference datasets. Please email meichen@live.unc.edu if you have more questions. Thank you!