Segments with tcn.em=2 and lcn.em=NA?

[lisemangiante]

Hi all, First of all, thank you for this tool, we found it very useful for our samples! I had a interpretation question from the facets output columns tcn.em and lcn.em: under which conditions the output can give for one individual segment tcn.em=2 and lcn.em=NA? If the caller was not able to determined the lowest CN, does it mean that, having tcn.em=2 and lcn.em=NA corresponds to either neutral LOH or no CN change (since if tcn.em=2 lcn.em can be either equal to 0 or 1) and, consequently, do you confirm that it would be safer to reject them from the list of segments with CN change since they are potentially normal and since we don't want to enrich for CNV false positive?

Very sorry if you've already answered to these questions before and I missed it.

Thank you again, Lise