Week #3 - Inside an FCS File

[UMGCCCFCSR]

This is the general discussion thread for Week #3, inside an .fcs file. It is a catch-all for all non-Q&A / open discussion.

[kushekhar]

Hi, I wanted to pull CytometryInR to week03 after syncing in github.
I couldn't pull, some error interms of branch or someting. Since, there were many uncommited files in 'changes', I tried commit and sync before pull thats was not possible either.
I got this error message.
Please help.
Thanks, Kushi

[UMGCCCFCSR]

Hi @kushekhar, can you take a screenshot of the entire commit graph, trying to see where the fork occurred. Do you have any files within the CytometryInR folder outside of a homework folder that you created? Best- David

[kushekhar]

Hi @DavidRach, here is the screenshot, I already see some fork, don't know what to do. To my knowledge, I did not put any files or folder in CytometryInR. I also see a new file is in the Changes now (2nd screenshot).
Kushi

[minhai2]

Hi David,

I was following the instructions to read the FCS files, but I received the error:

"CellCounts3L_AB_02_INF052_00.fcs" is not a valid file.

When I open the forked FCS file in the editor, it appears as garbled content. However, I am unable to successfully read it using the provided instructions.

Are there any alternative methods or recommended approaches to properly read this FCS file?

Thanks,
Min

[DavidRach]

Hi @minhai2, yeah, anytime I accidentally click on an .fcs file in Positron, they appear that way. Positron is not able to read them natively, so is trying to apply some other file format syntax with limited effect.

As far as the error, did you use "full.names=TRUE" in list.files()? That error can also results when read.FCS is not able to read your file path from your working directory to the file of interest. After copying the file over to your own project folder, see if the error still occurs when the file is in the working directory (top level of project folder) vs within the data subfolder.

Let me know if that works!

Best-
David

[DavidRach]

Oh wait, potential alternative if they were supposed to be the same file, in screenshot different file names ( 4L vs 3L) vs the one in the console.

[minhai2]

Thanks David! Adding "full.names=TRUE" in list.files() helped!