[BioC] Problem with SPILL matrix / keyword when using write.FCS and flowCore?

Robert Bruggner bruggner at stanford.edu
Tue Sep 25 19:40:20 CEST 2012


I think I am having trouble getting the SPILL keyword to be properly written in the header of an FCS file when I use the write.FCS() function in the flowCore package. 

For example, I will read in an FCS file and matrix associated with the SPILL keyword appears to be correctly formed. I will then write the unmodified FCS file back out using the write.FCS() function, read that newly written file back in using read.FCS(), and now, the matrix associated with the SPILL keyword appears to be malformed.

The code looks like this: 

a = read.FCS("a.fcs")

# SPILL matrix appears to be correct

# Write to file

# When I read the file back in, the SPILL matrix appears to be malformed. 
b = read.FCS("b.fcs")

Is there something I need to do differently when writing the FCS file? Also, happy to provide the offending FCS file if that would help. 

Thank you for any suggestions!


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