User: Angelos Armen
Angelos Armen • 0
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Posts by Angelos Armen
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... In the documentation of `scran::pairwiseWilcox`, it says that:
> The weight for the p-value in a particular level of block is defined as N_xN_y, where N_x and N_y are the number of cells in clusters X and Y, respectively, for that level.
This is reasonable but I was wondering if it's common pr ...
written 10 weeks ago by
Angelos Armen • 0
• updated
10 weeks ago by
Aaron Lun • 25k
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... In the [merging vignette][1] of `compareSingleCell`, `var.tech` is computed by `combineVar` within `multiBlockVar`. `combineVar`, however, returns mean variances across batches. Shouldn't [pooled variances][2] be returned instead?
[1]: https://github.com/MarioniLab/compareSingleCell/blob/master/ ...
written 3 months ago by
Angelos Armen • 0
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... > Is it? Looks like it's being called with universe.
Sorry my bad, you're right. ...
written 3 months ago by
Angelos Armen • 0
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... > multiBatchNorm() is called on the universe of all common genes, not just the HVGs. This is actually important to reduce the risk of violating the non-DE assumption between batches.
Sorry I meant to write
> genes with positive biological variance in any batch should be selected before calli ...
written 3 months ago by
Angelos Armen • 0
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... In the `simpleSingleCell` *Correcting batch effects* [vignette][1] spike-ins are available. What is the recommended workflow in the absence of spike-ins? I understand that `makeTechTrend` should be applied to each batch separately and then genes with positive biological variance in any batch should ...
written 4 months ago by
Angelos Armen • 0
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3 months ago by
Aaron Lun • 25k
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... In the *Feature selection across batches* section of the `simpleSingleCell` *Correcting batch effects* [vignette][1], genes with positive average (across batches) biological variance are selected. What is the reasoning behind that? Why aren't genes with positive biological variance in any batch sele ...
written 4 months ago by
Angelos Armen • 0
• updated
4 months ago by
Aaron Lun • 25k
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Comment:
C: k argument in buildSNNGraph
... > If you have a subpopulation with fewer than k+1 cells, buildSNNGraph() will forcibly construct edges between cells in that subpopulation and cells in other subpopulations. This increases the risk that the subpopulation will not form its own cluster as it is more interconnected with the rest of ...
written 4 months ago by
Angelos Armen • 0
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... In the documentation of buildSNNGraph it says that
> The choice of k can be roughly interpreted as the minimum cluster size.
Can I have an explanation for this please. ...
written 4 months ago by
Angelos Armen • 0
• updated
4 months ago by
Aaron Lun • 25k
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... Yes that makes sense. I was thinking of cell hashing used merely to multiplex samples from different donors and/or conditions. In that case, inter-sample and intra-sample doublets would form separate clusters (as cells would cluster by sample) and your strategy wouldn't be applicable. To take full a ...
written 4 months ago by
Angelos Armen • 0
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... Thank you for the detailed reply Aaron. The problem with cell hashing and multiplexed genotypes is that they can only detect inter-sample doublets; intra-sample doublets go undetected. Therefore computational approaches are still needed. ...
written 4 months ago by
Angelos Armen • 0
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