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marcelTBI / CNV_data

Data for training of CNV caller
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Problem in handling Negative values in the loess-normalized bin data #5

Closed meghavarshney closed 9 months ago

meghavarshney commented 9 months ago

How to address the presence of negative values in the loess-normalized bin data when conducting PCA training using this tool. These negative values are impacting the PCA training process, and how to handle them effectively within the tool's framework

marcelTBI commented 9 months ago

I know that there is a small number of negative values in loess-normalized bin data, but we did not compensate or treat them any differently. Maybe we should. However, there is only a very small number of negative value bins (usually up to 10 bins), so I believe the impact of treating them any differently would be very minor.