I am trying to get an estimation of the number of single cell clusters exist in my data. My code is as follows:
primedsce <- SingleCellExperiment(assays = list(counts = primedData)) primedsce <- calculateQCMetrics(primedsce,feature_controls = list(ERCC=primedmatchesERCC,MT = primedmatchesMT)) exprs(primedsce)<-log2(counts(primedsce)+1) primedsce <- sc3_prepare(primedsce,ks = 2:5) primedsce <- sc3_estimate_k(primedsce)
After running estimate_k, I will get this error:
Error in eigen(sigmaHatNaive, symmetric = TRUE, only.values = TRUE) :
infinite or missing values in 'x'
All of the values in count are either 0 or a real number. None are infinite. When I was looking at the reference code for sc3, I saw this "# important: normcounts have the same zeros as raw counts (fpkm)." Can anyone clarify what this comment means or explain what I am doing wrong?