User: Angelos Armen

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Posts by Angelos Armen

<prev • 11 results • page 1 of 2 • next >
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Stouffer's method weights in scran::pairwiseWilcox
... 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 ...
scran written 10 weeks ago by Angelos Armen0 • updated 10 weeks ago by Aaron Lun25k
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Comment: C: Feature selection across batches in simpleSingleCell when spike-ins are not avai
... 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 Armen0
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Comment: C: Feature selection across batches in simpleSingleCell when spike-ins are not avai
... > Is it? Looks like it's being called with universe. Sorry my bad, you're right. ...
written 3 months ago by Angelos Armen0
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Comment: C: Feature selection across batches in simpleSingleCell when spike-ins are not avai
... > 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 Armen0
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Feature selection across batches in simpleSingleCell when spike-ins are not available.
... 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 ...
simplesinglecell written 4 months ago by Angelos Armen0 • updated 3 months ago by Aaron Lun25k
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Feature selection across batches in simpleSingleCell "Correcting batch effects" vignette
... 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 ...
simplesinglecell written 4 months ago by Angelos Armen0 • updated 4 months ago by Aaron Lun25k
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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 Armen0
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k argument in buildSNNGraph
... 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. ...
scran written 4 months ago by Angelos Armen0 • updated 4 months ago by Aaron Lun25k
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Comment: C: Preprocessing in scran::doubletCells
... 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 Armen0
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Comment: C: Preprocessing in scran::doubletCells
... 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 Armen0

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