Problems with FLOWAI
2
0
Entering edit mode
msoares • 0
@edf9c9f6
Last seen 2.8 years ago
Portugal

Hi, I´m totally unproficient in R, but need to use it to run some FLOWJO pluggins. I have been having lots of problems with FlowAI. The error message on flowjo says: "FLOWAI Bioconductor error" Flow AI has failed to produce the expected derived paramenter. I ran the lines of code in the bioconductor website for FLOWAI without any apparent problems.

Here is the R

if (!requireNamespace("BiocManager", quietly = TRUE))

  • install.packages("BiocManager") Bioconductor version 3.12 (BiocManager 1.30.12), ?BiocManager::install for help BiocManager::install() Bioconductor version 3.12 (BiocManager 1.30.12), R 4.0.5 (2021-03-31) Old packages: 'pcaPP' Update all/some/none? [a/s/n]: a

There is a binary version available but the source version is later: binary source needs_compilation pcaPP 1.9-73 1.9-74 TRUE

Binaries will be installed trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/pcaPP_1.9-73.zip' Content type 'application/zip' length 529201 bytes (516 KB) downloaded 516 KB

package ‘pcaPP’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\ajdso\AppData\Local\Temp\RtmpYLNmqp\downloaded_packages

BiocManager::install("flowAI") Bioconductor version 3.12 (BiocManager 1.30.12), R 4.0.5 (2021-03-31) Installing package(s) 'flowAI' trying URL 'https://bioconductor.org/packages/3.12/bioc/bin/windows/contrib/4.0/flowAI_1.20.1.zip' Content type 'application/zip' length 4819112 bytes (4.6 MB) downloaded 4.6 MB

package ‘flowAI’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\ajdso\AppData\Local\Temp\RtmpYLNmqp\downloaded_packages Old packages: 'pcaPP' Update all/some/none? [a/s/n]: install.packages("png")a Update all/some/none? [a/s/n]: a

There is a binary version available but the source version is later: binary source needs_compilation pcaPP 1.9-73 1.9-74 TRUE

Binaries will be installed trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.0/pcaPP_1.9-73.zip' Content type 'application/zip' length 529201 bytes (516 KB) downloaded 516 KB

package ‘pcaPP’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in C:\Users\ajdso\AppData\Local\Temp\RtmpYLNmqp\downloaded_packages

Any help on this would be very wellcome!


# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )
flowAI • 2.8k views
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0
Entering edit mode

I too encountered issues with FlowAI errors in FlowJo. Fortunately, I managed to resolve this by designating the nearest path for both the wsp and FCS files within the system. This has been working seamlessly for me. To assist others facing similar challenges, I've created a YouTube tutorial. You can watch the tutorial here:

I hope you find these resources helpful!

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SHASHI • 0
@d627dbb5
Last seen 4 months ago
United States

Additionally, if you're looking to clean FCS data files, you can utilize an R script. I've prepared a comprehensive YouTube tutorial to aid everyone in this process.

Watch the R Script Tutorial for FCS Data File Cleaning here:

I hope you find these resources helpful!

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Alexander • 0
@399a612b
Last seen 11 weeks ago
United States

Hi. The length of the file path, or whether the files are local on the computer has nothing to do with it in my experience. I watched the above video and the suggestions made were unhelpful in my situation. My problem was that the appropriate file path is not what shows in Terminal on mac to tell FlowJo where R is located. The correct file path for Mac users is /usr/local/bin/R (only after you have installed R to your Applications folder). You can find more information directly from FlowJo at this link: https://docs.flowjo.com/flowjo/plugins-2/installing-plugins/. Hope this helps!

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