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Replace vst with batch removal #127

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LeaSeep opened this issue Mar 13, 2023 · 3 comments
Closed

Replace vst with batch removal #127

LeaSeep opened this issue Mar 13, 2023 · 3 comments

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@LeaSeep
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LeaSeep commented Mar 13, 2023 

mat <- assay(vsd)
mm <- model.matrix(~condition, colData(vsd))
mat <- limma::removeBatchEffect(mat, batch=vsd$batch, design=mm)
assay(vsd) <- mat
plotPCA(vsd)
@PaulJonasJost
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Does VSD always have a batch, even if we did not Define one?

@LeaSeep
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LeaSeep commented Dec 18, 2023

No - not that I'm aware of

@LeaSeep
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LeaSeep commented Jun 28, 2024

solved by @PaulJonasJost in #195

@LeaSeep LeaSeep closed this as completed Jun 28, 2024
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@PaulJonasJost @LeaSeep