Error with the compensation imc_comp_txt_example.Rmd script

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Computational image analysis of multiplexed Imaging Mass Cytometry acquisitions
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LaraW
Posts: 1
Joined: Fri Apr 23, 2021 7:30 pm

Error with the compensation imc_comp_txt_example.Rmd script

Post by LaraW » Fri Apr 23, 2021 10:15 pm

Hi everyone,

I am pretty new to working with R and tried to use to imc_comp_txt_example.Rmd from GitHub (https://github.com/BodenmillerGroup/cyT ... nvironment) script to compensate my IMC data vom CyTof. I use Windows 10. I run R 4.0.5. and work with RStudio and I installed the latest version of CATALYST 1.14.0.

It works fine until I reach Line 72 in the script. I run img_comp = comp_datimg(img, sm = sm) and it gives me the following error:

Fehler in (function (cond) : Fehler bei der Auswertung des Argumentes 'object' bei der Methodenauswahl für Funktion 'exprs': is(u$x, "SingleCellExperiment") is not TRUE
(sorry for using German here)

I have tried a lot of things, but since I have no experience with R I have absolutely no idea how to solve this problem. Since the program tells me that SingleCellExperiment is not true, I tried to install the SingleCellExperiment package again. It just tells me, that this package is already used and nothing changes. I also searched the internet about this problem, but I could not find any solution how to solve this.

Do you have any idea how to solve this problem?

Thanks in advance!

Lara
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