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navinlabcode / copykat

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Error in hclust(d, method = "ward.D2") : #74

Open qiangfan2022 opened 2 years ago

qiangfan2022 commented 2 years ago

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,

ErfanMowlaei commented 1 week ago

@qiangfan2022 Your input matrix most possibly has either negative or nan values. That was the case with my data.