Unexpectedly high log2 ratios for some but not all samples

[zetamui]

I have tried to compare the samples with or without this issue but couldn't find anything that could be the reason. Apart from ploidy # are there other reasons that could contribute to this unexpected high observed log2 ratio?

Best, Zeta

[etal]

Are the high log2 ratios in the bin-level data (.cnr files) or segments (.cnr files)? Were the ratios high for all data points, or just a few? If you can post a scatter plot here, that would be helpful to triage your issue.

[zetamui]

This is a sample with normal values (most values close to 0): The cnr log2 values density: The cns log2 values density:

All of these samples below have unexpected higher ratios (some not as high as others)

This sample named Abnormal 3 has an average of 2.79:

The cnr log2 values density: The cns log2 values density:

This sample named Abnormal 2 has an average of 0.72:

The cnr log2 value density: The cns log2 value density

This sample named Abnormal 4 has an average of 1.28: The cnr log2 values density: The cns log2 values density:

This sample named Abnormal 1 has an average of 0.85:

The cnr log2 values density: The cns log2 values density:

Thank you so much for your patience!