Hello List,
I've noticed some recent problems with file formatting exported from flowjo
with the concatenate function. I did some searching and found that this was
a recent feature, and unfortunately I am unable to import my concatenated
files into flowCore.

In short, header files are strangely broken between the point when they come
out of "concatenate" from flowjo and are read into flowCore.

temp <- read.FCS('myfile.fcs')
Error in readFCSgetPar(x, "$BYTEORD") :
  Parameter(s) $BYTEORD not contained in 'x'

I tried the fix posted previously for reading flowjo outputted files, but i
think this may be a different case. Opening the file in a basic text editor
shows some different formatting issues that may or may not be causing this
problem.

Sadly, I need to analyze the combination of these files, and not the
individual files alone, hence the use of the "concatenate" function.

My questions are as follow:

(1) is it possible to read a text file (data only) as a flowSet? As a result
I could bypass the header errors from flowjo and just use my combined
dataset.
(2) does this issue pop up with anyone else? I submitted a ticket to flowjo,
but i would prefer to be able to analyze my combined data in flowCore asap
:)

Thanks to anyone who has any input on this matter!

Cheers,
~Tiffany Chen

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