User: mscherer

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mscherer50
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Posts by mscherer

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Error in Heatmap creation with RnBeads
... Hi! to your questions: - For the heatmaps, you can use a combination of RnBeads' functions (e.g meth(rnb.set)) and a heatmap plotting function such as pheatmap, ComplexHeatmap, or heatmap.2 - Why it does run for the ```rnb.run.analysis``` command, but not for the exploratory module individually, ...
written 4 weeks ago by mscherer50
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Comment: C: Error in Heatmap creation with RnBeads
... Hi. The issue is probably in the plotting itself, and not in the computations. In the *execute* commands, there is not plotting involved, while in the *run* commands there is. Plotting heatmaps can be a challenging tasks on its own, in case there are many CpGs/regions to be plotted. I guess this is ...
written 4 weeks ago by mscherer50
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Answer: A: Error in Heatmap creation with RnBeads
... Hi! The very likely reason causing the program crash is a memory issue, i.e. RnBeads does not have sufficient main memory to perform the computations. This can especially occur in the clustering/heatmap part, since the heatmaps can be quite big. You have two potential solutions: - Try it with a n ...
written 4 weeks ago by mscherer50
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Answer: A: Run RnBeads with 'bismarkCytosine' files
... Thanks for reporting this. We are currently facing some issues with the bismarkCytosine import (see also the Issue reported here https://github.com/epigen/RnBeads/issues/7), but are working on fixing this. However, there should be an easy workaround: Instead of using the 'bismarkCytosine' option, u ...
written 6 weeks ago by mscherer50
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Answer: A: load.rnb.set throws multiple warnings when uploading an object
... I will try to answer you questions, but I should comment that the things you report are not really common. Parts of this answer are also wild speculations. **Question 1:** The warning/error message is shown, in case there is an issue with the clustering/distance metric of the clustering using the ` ...
written 9 weeks ago by mscherer50
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Answer: A: load.rnb.set throws multiple warnings when uploading an object
... Dear Assa, Sorry for the delay in replying to your question. You are facing a quite common issue that occurs from RnBeads' behavior of storing large matrices on disk using the ff-package. After multiple loadings and savings of the same object to/from disk, the error with file permission that you r ...
written 9 weeks ago by mscherer50

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Scholar 4 weeks ago, created an answer that has been accepted. For A: Error in Heatmap creation with RnBeads

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