Hello,
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:
Estimating k...
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?
I sent you the dataset, it is rather large though. Thank you for any help you can give me!
have you been able to reproduce the error?
Very sorry, have been busy resubmitting a paper, will get back to this issue this week. Hope it's ok for you. Sorry again.
Of course! No rush!