Incoherent values of LogR estimate & Total Copy number estimate

[Pacomito]

Hello, I ran FACETS on tumor vs normal in human (breast cancer). On chromosome 2 I have values for LogR estimate and Total Copy number estimate that I don't understand: cnlr.median = -0.41267360 & tcn.em = 3 for segment chr2:215595645-242039198. Assuming my normal is diploid, for a total copy number of 3 in the tumor, I should have a logR value around log2(3/2) ~ 0.58 , which is very different from -0.41.

Cellular fraction for this segment is 0.73. The purity is 0.94 & Ploidy is estimated to 2.6 .

Is there something I didn't understand ? Thanks ! Pacôme

[veseshan]

The information is insufficient to decipher what may be going wrong.

[Victoria-zz]

Hi. Have you figured this out? I have the same puzzle.