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

<prev • 34 results • page 2 of 4 • next >
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... 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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718
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... 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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written 22 months ago by Vladimir Kiselev150
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... 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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532
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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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... 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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441
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... Found an answer here: https://github.com/drisso/SingleCellExperiment/issues/1 ...
written 2.0 years ago by Vladimir Kiselev150
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441
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... Hi! Is there any reason why counts() method is not exported from the SingleCellExperiment package? The same applies to assay() method? Thanks you! ...
written 2.0 years ago by Vladimir Kiselev150
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... 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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... 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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