Week # 7 - General Discussion Thread

[UMGCCCFCSR]

This is the Week # 7 - Applying Transformations General Discussion thread.

Wondering how to determine optimal argument values when your instrument acquisition software is being uncooperative? Wondering why R displays everything in a new scale from 50 - 250 instead of the biexponential log tick marks your PI is expecting? This is the thread for you!

[anushans555]

Hi, just catching up on week 7 content. When I try to read the MC files into the GatingSet Object, I get the following error message. I tried updating my version of R and the packages. Any suggestions?

[DavidRach]

Hmm, based on the return outputs and your screenshot, your file.path looks to be set up correctly. Can you retry loading into GatingSet just in case it was something bizarre?

library(flowWorkspace)
MC_cytoset <- load_cytoset_from_fcs(MC_Files, truncate_max_range=FALSE, transformation=FALSE)
MC_GatingSet <- GatingSet(MC_cytoset)
MC_GatingSet

If it works, you should get back the regular GatingSet containing 3 files message. If you get back the error, then we will need to go back to the drawing board

[anushans555]

I tried again using your code, I still got the same error, as in the screenshot. Not really sure what is going on.

[anushans555]

I think I have fixed it by reloading the CytometryinR folder into Positron. When I was trying to resume catching up on the week 8 and 9 material, it wasn't pulling the new content into Positron even though I synced the fork in Github. So I reloaded everything into Positron using a new folder. It is now working. Not sure what the original problem was. Here is the screenshot to show the commands now work:

[DavidRach]

Hi @anushans555, glad that you got it to work. My guess was the original .fcs files got corrupted somehow at some point, which was resulting in the error. The start fresh approach bringing the data back in from the repository is a good one, I have had to do it a couple times for various folders as well. Will keep my fingers crossed everything continues to cooperate! Best- David

[anushans555]

Hi David,
You are probably right about the file being corrupted. Good to know it has happened before. At least I know for next time.
Fingers crossed indeed and thanks for your help!
Anusha