I'm trying to use FlowCore to match the gate names between several experiments that used the same antibodies. I have created a flowSet from each experiment and verified that the channel names match, but new .fcs files generated by

    write.flowSet()

doesn't pass the right channel desc to the resulting files. For example:

                      name   desc  range minRange maxRange
    $P2              FSC-A   <NA> 262144  -111.00   262143
    $P5              SSC-A   <NA> 262144     0.00   262143
    $P8             FITC-A CD45RA 262144  -111.00   262143
    $P9               PE-A  FOXP3 262144  -111.00   262143
    $P10    PE-Texas Red-A    CD4 262144  -111.00   262143
    $P11          PE-Cy5-A    CD8 262144  -111.00   262143
    $P12     PerCP-Cy5-5-A  TNF-a 262144  -111.00   262143
    $P13          PE-Cy7-A  IFN-g 262144  -111.00   262143
    $P14    Pacific Blue-A    CD3 262144   -82.08   262143
    $P15          AmCyan-A   CD25 262144  -111.00   262143
    $P16        Qdot 605-A    IL4 262144  -111.00   262143
    $P17             APC-A   CD69 262144  -111.00   262143
    $P18 Alexa Fluor 700-A    IL2 262144  -111.00   262143
    $P19         APC-Cy7-A  IL17A 262144  -111.00   262143

becomes

                      name   desc  range minRange maxRange
    $P1              FSC-A   <NA> 262144  -111.00   262144
    $P2              SSC-A   <NA> 262144  -106.95   262144
    $P3             FITC-A   <NA> 262144  -111.00   262144
    $P4               PE-A   <NA> 262144  -111.00   262144
    $P5     PE-Texas Red-A   <NA> 262144  -111.00   262144
    $P6           PE-Cy5-A   <NA> 262144  -111.00   262144
    $P7      PerCP-Cy5-5-A   <NA> 262144  -111.00   262144
    $P8           PE-Cy7-A CD45RA 262144  -111.00   262144
    $P9     Pacific Blue-A  FOXP3 262144  -101.76   262144
    $P10          AmCyan-A    CD4 262144  -111.00   262144
    $P11        Qdot 605-A    CD8 262144  -111.00   262144
    $P12             APC-A  TNF-a 262144  -111.00   262144
    $P13 Alexa Fluor 700-A  IFN-g 262144  -111.00   262144
    $P14         APC-Cy7-A    CD3 262144  -111.00   262144

How do I ensure the channels retain the right descriptions?

EDIT: After working with this some more, I have gotten as far as finding that the problem lies in the column.pattern="-A" argument I used in the original read.flowSet() call: it looks like the original parameter numbers (2-19) aren't getting passed to write.FCS(), resulting in misaligned channel descriptions. Still haven't figured out how to fix it.

I've pushed the fix to github and Bioc Devel branch.

devtools::install_github("RGLab/flowCore", ref = "trunk")