Hi, 

I have a folder containing .fcs files that I'm trying to import using read.flowSet() with:

all_data <- read.flowSet(path=fcs_dir_name,
                         pattern='*.fcs',
                         transformation=F);

This gives me the following error: 

Error in dim(colNames) <- c(ncol(from[[frameList[[1]]]]), length(frameList)) : 
  dims [product 125] do not match the length of object [25]

But running read.FCS() with lapply() on the same folder seems to work fine:

all_data<-lapply(list.files(fcs_dir_name,full.names=T),
                 function(x)read.FCS(x,transformation=F));

Any ideas on why this might be happening?

Thanks!

Ah you're right! I couldn't coerce it into a flowSet no matter what I tried. Turns out one of the samples had only one fluorescence channel instead of two. Is there any way to get read.flowSet() to only import specified channels?

Thank you!