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Heatmap output doesn't seem consistent with expected output #43

Closed suneetz closed 2 years ago

suneetz commented 3 years ago

Hi, im using copyKAT on a pediatric brain tumor scRNA seq sample and the output i have obtained with heat map shows 25% aneuploid and 75% diploid cells which doesn't seem consistent with a brain tumor sample (I would expect a much higher distribution of tumor cells). I tried the cell.line = "yes" to account for the sample potentially having one type of cell but I encountered an error and was unable to run it. Any thoughts on why I am encountering this type of result with my data?

gaobio commented 2 years ago

Hi, im using copyKAT on a pediatric brain tumor scRNA seq sample and the output i have obtained with heat map shows 25% aneuploid and 75% diploid cells which doesn't seem consistent with a brain tumor sample (I would expect a much higher distribution of tumor cells). I tried the cell.line = "yes" to account for the sample potentially having one type of cell but I encountered an error and was unable to run it. Any thoughts on why I am encountering this type of result with my data?

Please double-check using some known brain tumor markers to confirm whether there are aneuploid (tumor cells) missed.