The definition of "not.defined" in the copykat result

[suanzaoren]

Hello, developer of the CopyKAT program, I am very grateful for your development of this software.

I have a question now. After I execute the copykat function, the pred_result I obtain contains "not.defined" labels.

I have reviewed the previous questions and answers. This is because the copykat program performed filtering and did not conduct copykat analysis on it.

However, this raises a problem: for these cells with "not.defined" labels, in the subsequent analysis, should I define them as ordinary epithelial cells or should I define them as tumor cells?

[ConDem94]

Hello, developer of the CopyKAT program, I am very grateful for your development of this software.

I have a question now. After I execute the copykat function, the pred_result I obtain contains "not.defined" labels.

I have reviewed the previous questions and answers. This is because the copykat program performed filtering and did not conduct copykat analysis on it.

However, this raises a problem: for these cells with "not.defined" labels, in the subsequent analysis, should I define them as ordinary epithelial cells or should I define them as tumor cells?

Hi, did you find a solution to this?

[suanzaoren]

Hello, developer of the CopyKAT program, I am very grateful for your development of this software.
I have a question now. After I execute the copykat function, the pred_result I obtain contains "not.defined" labels.
I have reviewed the previous questions and answers. This is because the copykat program performed filtering and did not conduct copykat analysis on it.
However, this raises a problem: for these cells with "not.defined" labels, in the subsequent analysis, should I define them as ordinary epithelial cells or should I define them as tumor cells?

Hi, did you find a solution to this?

No, I haven't received the necessary assistance and response yet.