I have :

fcs <- lapply(dir("raw/FL/", full.names=TRUE, pattern = "\\.LMD$"),read.FCS)

>fcs

[[1]]
flowFrame object 'M340220834.LMD'
with 36424 cells and 13 observables:
             name          desc range minRange maxRange
$P1    FS INT LIN            FS  1024 0.000000     1023
$P2    SS INT LIN            SS  1024 0.000000     1023
$P3   FL1 INT LOG    CD103 FITC  1024 1.000922    10000
$P4   FL2 INT LOG       CD10 PE  1024 1.000922    10000
$P5   FL3 INT LOG CD13 PE-CF594  1024 1.000922    10000
$P6   FL4 INT LOG     CD5 PC5.5  1024 1.000922    10000
$P7   FL5 INT LOG     CD11c PC7  1024 1.000922    10000
$P8   FL6 INT LOG     CD123 APC  1024 1.000922    10000
$P9   FL7 INT LOG    CD25 AA700  1024 1.000922    10000
$P10  FL8 INT LOG    CD19 AA750  1024 1.000922    10000
$P11  FL9 INT LOG       CD20 PB  1024 1.000922    10000
$P12 FL10 INT LOG       CD45 KO  1024 1.000922    10000
$P13         TIME          TIME  1024 0.000000     1023
363 keywords are stored in the 'description' slot

[[2]]
flowFrame object 'M340220834.LMD'
with 61877 cells and 7 observables:
            name       desc range minRange maxRange
$P1   FS INT LIN FS INT LIN  1024 0.000000     1023
$P2   SS INT LIN SS INT LIN  1024 0.000000     1023
$P3  FL2 INT LOG   CD180 PE  1024 1.009044    10000
$P4  FL4 INT LOG  CD5 PC5.5  1024 1.000922    10000
$P5  FL8 INT LOG CD19 AA750  1024 1.009044    10000
$P6 FL10 INT LOG    CD45 KO  1024 1.000922    10000
$P7         TIME       TIME  1024 0.000000     1023
273 keywords are stored in the 'description' slot

>fs1 <- as(fcs, "flowSet")

Error in dim(colNames) <- c(ncol(from[[frameList[[1]]]]), length(frameList))

How can make that work?

Do I have to add extra "empty" channels to the second flowFrame? How can I do that?

Thanks

If you just want to ignore those extra channels from the first sample,  then you can use 'column.pattern' argument to only read those common ones, e.g.

read.flowSet(dir("raw/FL/", full.names=TRUE, pattern = "\\.LMD$"), column.pattern = "([FS]S)|([2,4,8,10]$)")