User: Vladimir Kiselev

Reputation:
130
Status:
Trusted
Location:
Sanger Institute, Cambridge, UK
Website:
http://www.genat.uk/
Twitter:
wikiselev
Scholar ID:
Google Scholar Page
Last seen:
1 week, 2 days ago
Joined:
2 years, 1 month ago
Email:
v******************@gmail.com

Posts by Vladimir Kiselev

<prev • 26 results • page 1 of 3 • next >
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Answer: A: SC3 Package: marker genes and normal genes obtained from featureData
... Hi, I would recommend you to read more about receiver operating characteristic (https://en.wikipedia.org/wiki/Receiver_operating_characteristic). Genes in which area under the ROC curve is less than the threshold are closer to completely random guess than the ones above the threshold. If you reduce ...
written 9 days ago by Vladimir Kiselev130
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Answer: A: Batch effect removal before SC3?
... Hi, what does removeBatchEffect return? If it remove zeros from your matrix this is not good for SC3 gene filter, which removes genes that have either very high or very low number of zeros. So, if there are no zeros in your data after batch correction, please switch the gene filter off by setting ge ...
written 5 weeks ago by Vladimir Kiselev130
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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 6 weeks ago by Vladimir Kiselev130
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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 7 weeks ago by Vladimir Kiselev130
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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 9 weeks ago by Vladimir Kiselev130
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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 9 weeks ago by Vladimir Kiselev130
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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 12 weeks ago by Vladimir Kiselev130
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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 12 weeks ago by Vladimir Kiselev130
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Answer: A: counts method is not exported
... Found an answer here: https://github.com/drisso/SingleCellExperiment/issues/1 ...
written 4 months ago by Vladimir Kiselev130
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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 4 months ago by Vladimir Kiselev130

Latest awards to Vladimir Kiselev

Scholar 7 months ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts
Scholar 8 months ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts
Scholar 22 months ago, created an answer that has been accepted. For A: SC3 with latent variable corrected counts

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