Error in hclust(d, method = "ward.D2") :
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Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 32/100
- Issue type
- Bug
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- r
- Domain
- bioinformatics
Research direction
Start by reproducing the supplied copykat call in R and inspect the warnings from sqrt(rawmat3) and sqrt(rawmat3 + 1) before hclust(d, method = "ward.D2"). Determine which input values produce NA, NaN, or Inf and verify that step 4 completes without the hclust error; the report does not include the expression matrix or a named test file.
Written by the indexing model from the issue text.
Description
Sorry to bother you, when i run the following code:
copykat.test <- copykat(rawmat=expr, id.type="S", ngene.chr=5, win.size=25, KS.cut=0.1, sam.name="test", distance="euclidean", norm.cell.names="",output.seg="FLASE", plot.genes="TRUE", genome="hg20", n.cores=1)
[1] "running copykat v1.1.0"
[1] "step1: read and filter data ..."
[1] "27669 genes, 1366 cells in raw data"
[1] "10895 genes past LOW.DR filtering"
[1] "step 2: annotations gene coordinates ..."
[1] "start annotation ..."
[1] "step 3: smoothing data with dlm ..."
[1] "step 4: measuring baselines ..."
Error in hclust(d, method = "ward.D2") :
NA/NaN/Inf in foreign function call (arg 10)
In addition: Warning messages:
1: In sqrt(rawmat3) : NaNs produced
2: In sqrt(rawmat3 + 1) : NaNs produced
I wonder how to fix it?
Thanks,
- Dominant language
- R
- Stars
- 305
- Forks
- 66
- PR merge metrics
- No merged PRs in 30d
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