The fibroblast, EC, and myofibroblasts were also identified as tumor. What are the reasons for this result?

[gloriafight]

I'm using SCEVAN to analyze a tumor sample. However, when I use the total cells as input. The result is very strange.

The marker is shown in the figure. We can know that C4 is EC, C11 is fibroblast, C0 and C10 is Epithelial cell. I want to distinguish normal cells and malignancy cells in epithelial cells.
The code is as follows:
`count_mtx = cr@assays$RNA@counts

results <- pipelineCNA(count_mtx,sample = "aaaa", par_cores = 8)`

[AntonioDeFalco]

Is it possible to share the aaaaheatmap.png file generated by SCEVAN? Are you analyzing human or mouse sample?

[gloriafight]

Is it possible to share the aaaaheatmap.png file generated by SCEVAN? Are you analyzing human or mouse sample?
This is the heatmap.

It is human sample.

[AntonioDeFalco]

The separation obtained by copy number alteration seems quite correct (although because of the perhaps not very high sample quality the heatmap is not so clear). The classified malignant cells do indeed seem to have obvious common alterations on some chromosome types 1, 3, 7 and 10. What kind of tumor is it? In case you are sure that those cells are not cancer you can pass to SCEVAN all the cells that you think are confidently normal as parameter norm_cells to get a better classification.

Regards.

[gloriafight]

The separation obtained by copy number alteration seems quite correct (although because of the perhaps not very high sample quality the heatmap is not so clear). The classified malignant cells do indeed seem to have obvious common alterations on some chromosome types 1, 3, 7 and 10. What kind of tumor is it? In case you are sure that those cells are not cancer you can pass to SCEVAN all the cells that you think are confidently normal as parameter norm_cells to get a better classification.

Regards.

Thank you for your suggestion. The heatmap certainly looks like it. It is lung cancer. I can designate these cells as normal cells to try to define malignant cell. However, does this indicate that some normal cell types may also have aneuploid at certain sites on the chromosome. Or it is because of the 10X scRNAseq data. Or is this something else? This is really interesting.