can list of genes in the reference be the list of differential genes only?

olechnwin commented 5 months ago

Hi,

I have a question. In the reference files input for ABC model, can the list of genes be the differential genes only? I wonder if this is acceptable or if it biased the model somehow and should not be done.

Thank you in advance for your clarification!

atancoder commented 4 months ago

See Jesse’s response below

engreitz commented 4 months ago

You should include all genes in the ABC calculation (using our provided promoter file), and then filter later.

This is because the list of genes (esp. the list of promoters) affects which peaks are included in the initial calculation, which ends up affecting the scores. If you run using only the list of promoters that are differential, the absolute values of the scores will be different than what the model expects

On Tue, Apr 23, 2024 at 11:58 AM Anthony Tan @.***> wrote:

i think that would be fine as ABC scores would be normalized on a per gene basis anyways.

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olechnwin commented 4 months ago

Thank you so much for your insights!

broadinstitute / ABC-Enhancer-Gene-Prediction

can list of genes in the reference be the list of differential genes only? #212