Trying to import flow cytometry data into rstudio to analyze


Hey, I'm pretty new to R and r studio so I have a pretty basic question. I am trying to analyze flow cytometry data using Bioconductor but can't figure out how to import the .fcs files that I have on the desktop of my computer. I found how to read it into the program but I've run into this:

above is my attempt at the sample code I found and below is the sample code I found <- system.file("extdata", "0877408774.B08", package = "flowCore")
x <- read.FCS(, transformation = FALSE)

I pulled the sample code from the vignette of the flowCore package.

I'm not really sure what is going wrong since I'm not familiar with coding. I'm open to any suggestions on my lines of code or if there is a better way to import these types of files. Thanks!


You'll need to load the package like so:


and then run your code