User: Vladimir Kiselev

Reputation:
150
Status:
Trusted
Location:
Sanger Institute, Cambridge, UK
Website:
http://www.genat.uk/
Twitter:
wikiselev
Scholar ID:
Google Scholar Page
Last seen:
5 months, 1 week ago
Joined:
3 years, 9 months ago
Email:
v******************@gmail.com

Posts by Vladimir Kiselev

<prev • 34 results • page 2 of 4 • next >
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Answer: A: SC3_estimate_k formatting error?
... Hi!  I looked at your data and found that it is very shallowly sequenced. In fact there were about 40 cells with all zeros in your matrix. When estimating k SC3 scales the data and if all values are zeros they will become NA after scaling and that is exactly what it was complaining about. Therefore ...
written 21 months ago by Vladimir Kiselev150
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Comment: C: SC3_estimate_k formatting error?
... Very sorry, have been busy resubmitting a paper, will get back to this issue this week. Hope it's ok for you. Sorry again. ...
written 21 months ago by Vladimir Kiselev150
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Answer: A: SC3_estimate_k formatting error?
... Could you please share your dataset with me, so that I can reproduce your error? Please share it with vk6@sanger.ac.uk. ...
written 22 months ago by Vladimir Kiselev150
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Answer: A: Raw count data for SC3 and SingleCellExperiment set problem
... In addition to Aaron's answer, please note that SC3 operates on logcounts slot of the SingleCellExperiment object. So if you would like to cluster raw counts you need to write them directly to the logcounts slot when creating a SingleCellExperiment object (this step is also shown in the SC3 vignette ...
written 22 months ago by Vladimir Kiselev150
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Comment: C: SC3 gene clusters
... Hi Ahmed, Oh sorry, now I see what confused you. Clustering of genes on all heatmaps is done by default functionality of the `pheatmap` package (it has nothing to do with SC3): ?pheatmap::pheatmap() kmeans_k - the number of kmeans clusters to make, if we want to agggregate the rows before drawin ...
written 23 months ago by Vladimir Kiselev150
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Answer: A: SC3 gene clusters
... Hi Ahmed, SC3 does not perform gene clustering. It only clusters cells. Therefore there is no column in `fData` for that. `sc3_N_markers_clusts` column defines which cell cluster each gene is a marker for. Hope this helps, Cheers, Vlad ...
written 23 months ago by Vladimir Kiselev150
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Answer: A: counts method is not exported
... Found an answer here: https://github.com/drisso/SingleCellExperiment/issues/1 ...
written 2.0 years ago by Vladimir Kiselev150
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counts method is not exported
... Hi! Is there any reason why `counts()` method is not exported from the SingleCellExperiment package? The same applies to `assay()` method? Thanks you! ...
singlecellexperiment written 2.0 years ago by Vladimir Kiselev150
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Answer: A: Does SC3 correct counts for gene length?
... Hi, 1. SC3 does not correct for gene length, please use other tools for that. 2. Yes, you can use any units with SC3, it will always find some structure in your data. The thing is that if you don't normalise your data, or normalise it in a wrong way you will either get a wrong result or pick up a ...
written 2.0 years ago by Vladimir Kiselev150
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Comment: C: Monocle causes R session to crash
... Sorry, Martin, just noticed your question. We had this problem when running our course: http://hemberg-lab.github.io/scRNA.seq.course/pseudotime-analysis.html Namely, if I run this in RStudio (on any system): library(monocle) deng <- readRDS("deng.rds") cellLabels <- colnames(deng) d <- ...
written 2.2 years ago by Vladimir Kiselev150

Latest awards to Vladimir Kiselev

Scholar 2.2 years ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts
Scholar 2.3 years ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts
Scholar 2.3 years ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts
Scholar 3.5 years ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts

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