Control-FREEC, input for ploidy

[lethalfang]

Control-FREEC has an input for ploidy.

I wonder what is considered a better practice (ploidy=2 or ploidy=4) if I'm looking at a near-tetraploid cancer tissue like this in a tumor-normal pair:

http://www.path.cam.ac.uk/~pawefish/BreastCellLineDescriptions/HCC1143.html

The results are the output regions are a bit different for ploidy=2 and ploidy=4.
When I used ploidy=4, I get results called "loss" for copy numbers of 2 and 3. I'm not sure if I want copy numbers of 2 and 3 called "loss".

Should I use ploidy=2, or should I use ploidy=4 and then annotate "loss" and "gain" myself?

Thanks in advance if anyone can clarify.

[dingxiaofan1]

For tetraploid genome, cytogeneticsts always call CN> 3 as gain and CN< 3 as loss. You could treat those data as data obtained from plant's genome. But I am not very satistified with the ploidy option. Because when you set a ploidy value for control-pair sample, it means the P-copy for both of the control and tumor sample. But in fact not.