Cannot open Sysmex Partec Cube 6 .fcs (FCS3.0) with read.FCS

[mrescan]

Hello,

I am trying to read .fcs (FCS3.0) from a Sysmex Partec Cube 6 V2M flow cytometer, and get an error (with (R 4.2.1, flowCore2.10.0).

read.FCS('AEboth') returns (AEboth being one sample file):

Error in readFCSdata(con, offsets, txt, transformation, which.lines, scale, :
object 'dat' not found

With the function readFCS() from the IFC package, I can access to the data, but with a warning:

Warning: TEXT (or sup. TEXT) segment: can't find final delimiter
Warning: TEXT (or sup. TEXT) segment: can't find final delimiter
Warning: TEXT (or sup. TEXT) segment: supplemental TEXT segment is not readable:
embedded nul in string: 'PK\003\004\024\0\b\0\b\0\316|<WG\314\233B\312)\0\0\211[\001\0\024\0\0\0config/config_20.xsd\355}[s\032I\326\340\363N\304\374\207\034"v\333\356q!@\226\355\361\272\325\201%$1\215\004!\260\333=1\021\212\202J\240>\027UL]t\231\347\375K\273O\373\264\363\307\366\234\223\231u\201\252\242\n\201\204\272q\314E@^\3179y\362\334\363\323\317\3673\213\335r\3273\035\373\247J\275Z\2530n\217\034\303\264'?U\002\177\254}\250\374|\374\347?}\372\213\2461n\230>7\330\235\351O\331\267\313N\177\376\300n\033\265z\203\271\334\252\262\006{u\377\356\355k\366j\352\373\363\217\a\awwwU\335\362\235[\275:rf\257\331\360\201\235\272U\3267g\216\315:\272=\341\354UOw}>b\347\263\341\305k\246ij\242?\377\351\317\177:\267\234\241nq\217\365GS>\323\331\277\003\227\365\334\377\374\337q`O\230\301]v\362\345sK\373\305\261\307\346$pu\037\326\357\031\272\317Mncw\306\276\212M\261\217\254Q\255\341\027}_\267\r\306\360\213Z\375\350\246\366\376\24 [... truncated]

The file is here:
https://www.dropbox.com/scl/fi/3xk48ogmzdmjqx9gnkt1b/AEboth.fcs?rlkey=t8fud39ikvvqt9ju0n0ddf0p9&dl=0

Thank you for your help,

Best,

Marie

[SamGG]

Hi,
This FCS file is not handled by my flowCore 2.12.0.
Maybe the latest version could handle this format. Either try to upgrade https://bioconductor.org/install/ or wait for developers to answer.

In my 2.12.0 version, I ended up with the datatype being "integer" and fails the "numeric" test near

      bytes <- readBin(con = con, what = "raw", n = nBytes, 
                       size = 1)
      if (dattype == "numeric" && length(unique(size)) > 
          1) 
        stop("we don't support different bitwdiths for numeric data type!")

Browse[2]> dattype
[1] "integer"
Browse[2]>
size [1] 2 2 2 2 2 4 1