Hi, I´m trying to use flowSOM with an FCS file an i´m having problems with the read.FCS function:

I´m trying the following code:

filename <- system.file("extdata", 'fusionLMA.fcs', package="FlowSOM") ff <- flowCore::read.FCS('fusionLMA.fcs')

and obtained the following error:

Error in flowCore::read.FCS("fusionLMA.fcs") : 'fusionLMA.fcs' is not a valid file

I can´t figure out what´s wrong, since the file is an FCS file . . . ```

The error means the file doesn't exist, at least not in your working directory. Note that the file doesn't (shouldn't!) exist in your R library dir, so the first line of code doesn't make sense (the system.file part, which is meant to find extra data that the package author might use for examples or whatever).

If you do

file.exists("fusionLMA.fcs")

And it returns FALSE, then that file isn't in your working directory and you need to use setwd to change the working dir to wherever the file is, or provide the path to the file to read.FCS.