User: Andrzej Oleś

gravatar for Andrzej Oleś
Andrzej Oleś670
Reputation:
670
Status:
Trusted
Location:
EMBL Heidelberg, Germany
Website:
https://github.com/aoles
Twitter:
andrzejkoles
Scholar ID:
Google Scholar Page
Last seen:
1 month, 1 week ago
Joined:
5 years, 1 month ago
Email:
a***********@embl.de

Posts by Andrzej Oleś

<prev • 74 results • page 2 of 8 • next >
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Answer: A: Using BiocStyle with plotly
... Hi Lluís, thanks for your feedback! I had a look into sizing of plotly::ggplotly output and it seems that this is a more general issue which is present also for regular html_document format,  and not something specific to BiocStyle. The thing is that the produced output has fixed size and does not ...
written 4 months ago by Andrzej Oleś670
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Answer: A: EBImage cannot read .png images from Image.R
... Your description indicates a problem with either the input filename or downstream package functions calling EBImage functions. The quotation mark in the error message looks suspicious indeed, as it suggests that the filename passed to readImage wrongly contains a quotation mark, i.e. filename.png". ...
written 5 months ago by Andrzej Oleś670
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Answer: A: Issue with pandoc-citeproc when rendering the f1000 article Rmd file from BiocWo
... Hi Leo, there seems to be a problem with version compatibility between pandoc and pandoc-citeproc as described in the issue you linked. Apparently your pandoc-citeproc version is outdated, as on my linux machine I have a much more recent version of pandoc-citeproc 0.10.1 vs. yours 0.5 even though I ...
written 5 months ago by Andrzej Oleś670
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Comment: C: Error during EBImage installation
... For the record, Martin's solution applies to Debian based Linux distributions such as Ubuntu. On Red Hat Linux (e.g. Fedora) the system dependency can be obtained by yum install fftw-devel.   ...
written 5 months ago by Andrzej Oleś670
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Answer: A: Error during EBImage installation
... Dear Maarten, the output of your sessionInfo indicates that you are running R under OS X Sierra, but attempt to install packages from sources. Is there any particular reason why you don't use mac binaries? Platform-specific binary packages typically include the necessary dependencies, so you should ...
written 5 months ago by Andrzej Oleś670
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Comment: C: Focal stacking of images in R/EBImage
... Hi Phil, this method is now provided by the new Bioconductor package MaxContrastProjection. The package also implements the novel maximum contrast projection algorithm which avoids some of the problems of the former method and yields cleaner results. ...
written 7 months ago by Andrzej Oleś670
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Answer: A: get pixel coordinates interactively with EBimage
... It's possible to retrieve pixel coordinates interactively by using the function locator() in combination with the "raster" mode of display, as in the following example. library("EBImage") # load and display a sample image img <- readImage(system.file("images", "sample.png", package="EBImage")) ...
written 7 months ago by Andrzej Oleś670
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Answer: A: Deals with image value superior to 0,1 range
... Dear Valérian, you can save your images as 16 bit TIFFs and transform between the integer and double pixel representation on read/write. For this when saving your images you would divide the pixel values by the maximum value which can be stored as unsigned integer (UINT16), which is 2^16-1.  To tra ...
written 7 months ago by Andrzej Oleś670
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Comment: C: EBImage / problem in running the code via Rscript
... Thanks Martin, I basically came to similar conclusions. I was wondering what would be the best way of fixing this on our side. The problem seems to be related to the fact that methods package needs to be attached in order to manipulate S4 objects by abind, as running the following in Rscript also f ...
written 8 months ago by Andrzej Oleś670
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Comment: C: Workflow highthroughputassays can't install properly
... I assume you previously had a working installation of rgl, but probably because of some system changes (?) it stopped loading. The easiest thing to try is to re-install the package. install.packages(rgl)   ...
written 9 months ago by Andrzej Oleś670

Latest awards to Andrzej Oleś

Scholar 5 months ago, created an answer that has been accepted. For A: EBImage crashing in for-loop
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Only 1s created by erode()
Scholar 19 months ago, created an answer that has been accepted. For A: reactive CellCODE heatmap
Scholar 19 months ago, created an answer that has been accepted. For A: Not able to display actual grayscale image using EBImage
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Only 1s created by erode()
Scholar 19 months ago, created an answer that has been accepted. For A: EBImage read png causes R to crash
Scholar 19 months ago, created an answer that has been accepted. For A: EBImage crashing in for-loop
Scholar 19 months ago, created an answer that has been accepted. For A: EBImage crashing in for-loop
Scholar 2.0 years ago, created an answer that has been accepted. For A: EBImage crashing in for-loop
Scholar 2.4 years ago, created an answer that has been accepted. For A: EBImage crashing in for-loop

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