User: Andrzej Oleś

gravatar for Andrzej Oleś
Andrzej Oleś720
Reputation:
720
Status:
Trusted
Location:
Heidelberg, Germany
Website:
https://github.com/aoles
Twitter:
andrzejkoles
Scholar ID:
Google Scholar Page
Last seen:
2 months, 1 week ago
Joined:
6 years ago
Email:
a***********@embl.de

Posts by Andrzej Oleś

<prev • 83 results • page 1 of 9 • next >
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Answer: A: EBImage -- local machine VS cluster -- could not find function "slot"
... Thanks Mathieu for reporting this problem. I could reproduce the described behavior when trying to subset an image in a script executed through Rscript, see Issue #31. The issue is related to methods package not being loaded by Rscript. Until this is fixed please add a call to library(methods) at th ...
written 10 weeks ago by Andrzej Oleś720
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Comment: C: EBImage -- local machine VS cluster -- could not find function "slot"
... How exactly do you run your script on the cluster, do you call it in a different way than locally? ...
written 3 months ago by Andrzej Oleś720
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Answer: A: Unable to display image in browser from script
... Dear Liese, thank you for reaching out. The observed behavior is not an error, as display will show the image in a browser only if run from an interactive R session. When called from a script or from an R Markdown document it uses R's built-in graphics capabilities. As documented on the man page ?EB ...
written 3 months ago by Andrzej Oleś720
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Answer: A: Relabelling objects - EBImage
... Dear Mathieu, in order to re-label the specks you need to overlay the Voronoi partitions with the specks mask to extract the corresponding labels. The difficulty here is that occasionally a speckle might end up on the border of two or more partitions. You can account for such situations by assigning ...
written 4 months ago by Andrzej Oleś720
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Comment: C: Does BiocWorkflowTools package generate F1000Reseach/Bioconductor-stype PDF at o
... Actually, RStudio GUI allows you to switch between the different output formats defined in the document's YAML header. You can select them from the dropdown list which can be expanded by clicking on the small arrow next to "Knit". ...
written 4 months ago by Andrzej Oleś720
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Comment: C: Relabelling objects - EBImage
... Hi Mathieu, thank you for reaching out. Could you maybe share your files such that accessing them doesn't require setting up an account with a third-party service? Thanks! ...
written 4 months ago by Andrzej Oleś720
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Comment: C: How to Remove EBImage objects that have holes?
... Thank you Wolfgang for providing a solution to the problem. This is probably the way to go. Note that there is a dedicated function rmObjects to remove objects from images which is the preferred approach for performance reasons. It also provides an easy way to re-label objects such that the maximum ...
written 6 months ago by Andrzej Oleś720
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Comment: C: simpleRNASeq easyRNAseq warnings edgeR error
... Thanks for your patience. In order to proceed, could you maybe provide a self-contained MWE illustrating the issue? Maybe it's enough to share the .rda files referenced in your code. ...
written 9 months ago by Andrzej Oleś720
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Comment: C: simpleRNASeq easyRNAseq warnings edgeR error
... Thank you for reporting this. I will look whether there is anything which could be done on the DEFormats side to address this. I will get back to you as soon as I know more. ...
written 9 months ago by Andrzej Oleś720
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Answer: A: no floating figures with biocstyle
... There is a knitr code chunk option fig.pos meant for the purpose of controlling the placement of floats. When it is set to 'H' it will freeze the figure by unfloating it. Note the uppercase which is important because this is a special placement specifier which also requires the LaTeX package float t ...
written 12 months ago by Andrzej Oleś720

Latest awards to Andrzej Oleś

Popular Question 5 months ago, created a question with more than 1,000 views. For Updates to BiocStyle formatting
Appreciated 16 months ago, created a post with more than 5 votes. For Updates to BiocStyle formatting
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Issue with pandoc-citeproc when rendering the f1000 article Rmd file from BiocWo
Scholar 16 months ago, created an answer that has been accepted. For A: EBImage read png causes R to crash
Supporter 16 months ago, voted at least 25 times.
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Only 1s created by erode()
Scholar 16 months ago, created an answer that has been accepted. For A: EBImage crashing in for-loop
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Only 1s created by erode()
Scholar 16 months ago, created an answer that has been accepted. For A: EBImage crashing in for-loop
Scholar 2.5 years ago, created an answer that has been accepted. For A: EBImage crashing in for-loop
Scholar 2.5 years ago, created an answer that has been accepted. For A: EBImage read png causes R to crash
Scholar 2.5 years ago, created an answer that has been accepted. For A: Not able to display actual grayscale image using EBImage
Scholar 2.5 years ago, created an answer that has been accepted. For A: reactive CellCODE heatmap
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Only 1s created by erode()
Scholar 2.5 years ago, created an answer that has been accepted. For A: EBImage crashing in for-loop
Scholar 2.9 years ago, created an answer that has been accepted. For A: EBImage crashing in for-loop
Scholar 3.3 years ago, created an answer that has been accepted. For A: EBImage crashing in for-loop

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