Parameter finetuning for cell line

[aranham]

Hi Teng,

We ran Numbat on cell lines that have chr 1q gain or amplification by applying the procedure to detect and exclude clonal deletions/LOH prior to running Numbat. While the method works well and we see the subclonal architecture for chr1q in the normalized expression profiles, these are not properly called in the final panel.
Is there a parameter we can finetune to get concordant results between expression data and the final panel?

I am sharing the expression data and the final panel on email.

Thanks,
Michelle