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:
3 months, 1 week ago
Joined:
6 years, 6 months ago
Email:
a***********@embl.de

Posts by Andrzej Oleś

<prev • 87 results • page 1 of 9 • next >
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Comment: C: EBImage computeFeatures error
... Thank you Mathieu! Using the object files you provided I could reproduce the described error in a call to computeFeatures(Donut, Img488, xname = "Donut", refnames = "488", haralick.nbins = 32, haralick.scales = c(1, 2, 4, 8)) inside of ImageProcessing(Image = AllImages, Plate = 2, Well = "A5", Posit ...
written 4 months ago by Andrzej Oleś720
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Comment: C: EBImage computeFeatures error
... Please provide the actual R objects written with save rather than image files. Thanks! ...
written 5 months ago by Andrzej Oleś720
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Comment: C: EBImage computeFeatures error
... Thank you Mathieu! I'm not entirely sure yet what could be wrong. But according to the error message it seems that things fails when trying to cbind the results of computeFeatures.basic, computeFeatures.moment, and computeFeatures.haralick. So probably something goes wrong already when computing the ...
written 5 months ago by Andrzej Oleś720
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Comment: C: EBImage computeFeatures error
... I tried running Mike's script under Mac OS but couldn't reproduce the issue too. Mathieu, could you maybe run traceback() after you encounter the error and paste the output? Cheers, Andrzej > sessionInfo() R version 3.5.1 (2018-07-02) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running unde ...
written 5 months ago by Andrzej Oleś720
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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 8 months 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 9 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 9 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 10 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 10 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 11 months ago by Andrzej Oleś720

Latest awards to Andrzej Oleś

Popular Question 12 months ago, created a question with more than 1,000 views. For Updates to BiocStyle formatting
Appreciated 22 months ago, created a post with more than 5 votes. For Updates to BiocStyle formatting
Teacher 22 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 22 months ago, created an answer that has been accepted. For A: EBImage read png causes R to crash
Supporter 22 months ago, voted at least 25 times.
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Only 1s created by erode()
Scholar 22 months ago, created an answer that has been accepted. For A: EBImage crashing in for-loop
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Only 1s created by erode()
Scholar 22 months ago, created an answer that has been accepted. For A: EBImage crashing in for-loop
Scholar 3.0 years ago, created an answer that has been accepted. For A: EBImage crashing in for-loop
Scholar 3.0 years ago, created an answer that has been accepted. For A: EBImage read png causes R to crash
Scholar 3.0 years ago, created an answer that has been accepted. For A: Not able to display actual grayscale image using EBImage
Scholar 3.0 years ago, created an answer that has been accepted. For A: reactive CellCODE heatmap
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Only 1s created by erode()
Scholar 3.0 years ago, created an answer that has been accepted. For A: EBImage crashing in for-loop
Scholar 3.4 years ago, created an answer that has been accepted. For A: EBImage crashing in for-loop
Scholar 3.8 years ago, created an answer that has been accepted. For A: EBImage crashing in for-loop

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