The results of diploid and aneuploid are reversed in test_copykat_heatmap.jpeg, why?

[lj20220425]

Sorry to bother you, when I run the following code:
copykat.test <- copykat(rawmat=exp.rawdata,
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=4)
Sometimes, the results of diploid and aneuploid were logical in the test_copykat_heatmap.jpeg; while sometimes the results of diploid and aneuploid were reverse in the test_copykat_heatmap.jpeg. Which should be aneuploid , but titled with diploid. Can you tell me why this happend and how to solve it. Best wish

[tlesluyes]

Hi dev team,

Similar experience here, I feel like the diploid/aneuploid categories are swapped for some reason. I'm attaching a JPEG file. Please let us know how to fix this.

Cheers,

Tom.

[ZhangMH2000]

I encountered the same issue. I had to reverse the results manually.

[ZhangMH2000]

I found another issue: I repeated copykat for my dataset due to some test reason. The new output shows a correct result, and the heatmap was correct. However, there are some little differences between the two times, and the predicted result changed slightly in one sample(10% cells). I’m not sure whether it’s normal.

[gloriafight]

I had a similar problem. Some of normal cells are marked as malignant cells, and Some of malignant cells are marked as normal cells. However, through the clustering of Seurat, it can be found that malignant cells are clustered together.


The lower left corner is a malignant cells.

[kaizen89]

I also observe results being reversed on a sample among cells from tumor vs adjacent tissues (adjacent cells being classified as aneuploid). Unexpectdly, when I run copykat on merged samples (I assume batch effect) then most of the cells of adjacent tissue are classified as diploid.