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Add a positive control for the EMD metric #11

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rcannood opened this issue Jan 16, 2025 · 2 comments
Open

Add a positive control for the EMD metric #11

rcannood opened this issue Jan 16, 2025 · 2 comments
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enhancement New feature or request

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@rcannood
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@rcannood rcannood added the enhancement New feature or request label Jan 16, 2025
@ghar1821 ghar1821 self-assigned this Jan 16, 2025
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For EMD, we can do the following.

Since the metric will compute how well does the corrected sample 1 for donor A from batch 1 look like sample 2 for donor A from batch 2, most methods will make some changes to sample 1 to make it look more like sample 2. For positive control, we can just get it to return sample 2 instead of some form of corrected sample 1. This sample 2 will then be compared to the sample 2 and yield EMD of 0.

It is acceptable to have best possible EMD of 0 with the assumption that the difference between sample 1 and sample 2 are purely driven by batch effect because the two samples are technical replicates.

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