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What happens is that when the text and header part of an FCS file is one
less than a multiple of 256, cellquest inserts an extra separator "\"
followed by 255 spaces (at least this is the case for 767, I presume it
will be general), the pointers in the header are correct ie text end is
767, data start is 768, but the padding shifts the actual data start to
1024, this causes a frame shift mutation when the software starts trying to
read FSC for event one from totally the wrong position.
To fix files that have this problem, open them in Word, scroll to the end
of the text part and select the last "\" and the trailing spaces, delete
them and save the file as text. Running them through FACSconvert or FCS
Assistant should turn them into cellquest readable files.
An example follows:
=46CS2.0 256 767 768 868647 0 0 [padding spaces=
]
\$BYTEORD\4,3,2,1\$DATATYPE\I\$NEXTDATA\0\$SYS\Macintosh System Software
7.1.0\CREATOR\FACStation=81
1.0\$TOT\86788\$MODE\L\$PAR\5\$P1N\FSC-H\$P1R\1024\$P1B\16\$P1E\0,0\$P2N\SSC
-H\$P2R\1024\$P2B\16\$P2E\0,0\$P3N\FL1-H\$P3R\1024\$P3B\16\$P3E\4,0\$P4N\FL2
-H\$P4R\1024\$P4B\16\$P4E\4,0\$P5N\FL3-H\$P5R\1024\$P5B\16\$P5E\4,0\$P1S\For
ward Scatter\$P2S\Side Scatter\$P3S\CD45RB FITC\$P4S\CD4 PE\$P5S\CD8
Tricolour\SAMPLE
ID\DBA/2T-RB.4.8\$CYT\FACScan\$BTIM\15:54:10\$ETIM\16:03:24\$FIL\DBA/2T-RB.4
.8.019\$DATE\13-Jun-96\\ [padding spaces]
(data starts here)
Note the double slash which is a good indicator that something has gone
wrong (since it's forbidden by FCS2.0 except in the body of a value or
token.
To make sure that you get all of the spaces, get word to show them as dots
by selecting show paragraph mark on the view menu.
Note also that acquiring a files with a different filename length or sample
ID length or parameter number would cause the problem to come or go.
please contact me if B-d have cured this one, or if you want me to provide
a fix in FCS Assistant.
Ray
Ray Hicks
________________________________________________________________________
|University of Cambridge |Tel 01223 330149 |
|Department of Medicine |Fax 01223 336846 |
|Level 5, Addenbrookes Hospital |e-mail rh208@cus.cam.ac.uk |
|Hills Road Cambridge |Web Page/ facsmac.med.cam.ac.uk |
|CB2 |ftp server 131.111.80.78 |
|UK | |
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