BIG files

MURPHY@A.CFR.CMU.EDU MURPHY at A.CFR.CMU.EDU
Thu Jan 6 14:24:43 EST 1994


Doug Smoot writes:

>I have had a similar problem with my Elite.  I discovered that the problem
>in my files was in the header.  When I saved my files I got an error
>message saying the there was a problem saving the file for some reason I
>can not remember.  The FCS file format only allows for a certain size
>file.  I ran my files through an FCS file reading program we created and it
>determined that the data area was invalid (It has been a while but I think
>that is because there are not enough digits in the header space to allow
>for a very large data area.  What I now do is pregate the data using
>the listgate feature (under the options screen on the cytometer - useful if
>you are gating out non-indo loaded cells if you are running an indo
>experiment).  This doesn't really help with the files you have already saved
>though.

The size limitation on FCS files in unlikely to be the problem.  The
headers allow 8 digits for the offsets, which allows for listmode files
of around 24 million events of 4 parameters (1 byte/parameter), 12
million events of 4 parameters (1 word/parameter), or 6 million events
of 8 parameters (1 word/parameter).  However, particular implementations
of FCS often impose lower limits (especially for designs in which all
events must be stored in memory, rather than processed from disk as
needed).  For files already collected, contact a colleague with
a system capable of handling large files (e.g., Consort/VAX) and
have him/her chop the files into pieces or otherwise process them.
Another possibility is to use an editor to change the offsets and
value for the $TOT keyword to make the file "appear" smaller.

Bob Murphy




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