Error in step4
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 25/100
- Issue type
- Bug
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- r
- Domain
- bioinformatics
Research direction
The reported entry point is the copykat(...) call with the shown parameters; start by reproducing it and inspecting the step 4 baseline calculation and hclust error. Done means determining why the 15,946 known normal cells produce an invalid or oversized clustering input and documenting a verified resolution.
Written by the indexing model from the issue text.
Description
Sorry to bother you, when I run the following code:
copykat.NR <- copykat(rawmat=counts, id.type="S", cell.line="no", ngene.chr=5, win.size=25, KS.cut=0.15, sam.name="AML_NR", distance="euclidean", norm.cell.names=normal.ref, n.cores=20)
[1] "step 4: measuring baselines ..."
[1] "15946 known normal cells found in dataset"
[1] "run with konwn normal..."
[1] "baseline is from known input"
Error in hclust(d, method = "ward.D2"): the size cannot be NA, and the output cannot exceed 65536
Can you help me to solve this problem?
Thank you very much!
- Dominant language
- R
- Stars
- 305
- Forks
- 66
- PR merge metrics
- No merged PRs in 30d
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