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wikiselev
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... I don't think this is related to SC3. You can use the pheatmap package to visualise any genes you like. The heatmap will look similar to SC3, since it's also using pheatmap. ...
written 8 weeks ago by Vladimir Kiselev130
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127
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... Please refer to this GitHub issue: https://github.com/hemberg-lab/SC3/issues/60 ...
written 5 months ago by Vladimir Kiselev130
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... I am afraid I need to look at your dataset, could you please share it with me again? ...
written 5 months ago by Vladimir Kiselev130
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... 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 6 months ago by Vladimir Kiselev130
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... 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 7 months ago by Vladimir Kiselev130
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326
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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 7 months ago by Vladimir Kiselev130
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326
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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 7 months ago by Vladimir Kiselev130
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326
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written 8 months ago by Vladimir Kiselev130
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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 8 months 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 9 months ago by Vladimir Kiselev130