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You could coalesce the files using a word processor or spread sheet.
Assuming that all of the files have the same number of parameters and that
they're not too big for the program to handle, here's how:
FCS files are in three parts;
a HEADER that contains the FCS version and offsets from the beginning of
the file to the start and end of the other parts.
A TEXT part that contains information on number of parameters and their
names, number of events, sample ID etc.
a DATA part that in your case should contain the list mode data (the
following won't work for correlated (density or contour plot) or
uncorrelated (histogram) data.
Use "Open any file" in Microsoft Word 4 or choose "All Files" from the
"List files of type" menu in the "Open..." dialog of later versions to
access your files.
1)Open the second file, find the beginning of the data (the third number in
the header) and select all of the characters up to the end of the data part
(the fourth number in the header) note that there will probably be padding
spaces after the last "\" in the text part up to the first character of the
data, and you shouldn't select the paragraph mark at the end of the file -
word inserts that.
2)Copy this chunk, open the first data file, and paste the chunk after the
end of the data part in this file (before the last paragraph mark.)
repeat steps one and two for any remaining files.
You then need to update the number of events in the text part, and the
offsets in the header. To do this, find the string "$TOT" in the text part,
and change the value immediately after it to the new total, leave the "/"
characters alone, and don't hit return. If the new value has more digits
than the old, you either have to update the text end and data start and
data end offsets, OR delete the appropriate number of padding spaces
between the text and data part, and only update the text end value (the
second method is quicker and easier than the first if there are any padding
spaces, and you'll have to update the data end value later anyway).
The data end value can be found by selecting the whole document ("Select
All" in the "Edit" menu) and doing a word count (in the tools menu), the
value should be two less than the number of characters calculated by Word,
note that if there are more digits in the new number than before, you'll
have to delete the appropriate number of padding spaces immediately after
the number that you type in, otherwise the header will be the wrong size
(its size is fixed at 58 bytes), and the offsets will be invalid.
Lastly you should save the newly built file as TEXT with a new name (so
that you don't overwrite your original first file). Cellquest won't be
able to open the file directly and you'll have to change its macintosh type
and creator attributes, you can do this with either FCS Assistant
(available from my server below, a snip at $25 shareware) or with Geoff
Osborne's autotypers (snippier at $0 freeware) also available from my
server and other places.
If you're going to do a lot of this, and you register FCS Assistant (ie pay
me the shareware fee), I can incorporate a merge/coalesce function into FCS
Assistant.
If you need any clarification of the above, or if you can't get it to work,
drop me a line
Ray
At 9:00 am +1000 26/5/97, Adrian Smith wrote:
>Hi All,
> We are wondering if it is possible to combine FCS files. We have
>two or three files recorded on a Facstar Plus (HP system) that we want to
>combine so CellQuest will treat them as one file for the purpose of drawing
>dot plots. I know you can add histograms together in Cell Quest but we want
>to do something similar for dot plots. Any suggestions?.
>Thanks
>Adrian
>
>
>
>******************************************************
>Adrian Smith (PhD Student)
>T CELL BIOLOGY GROUP
>Centenary Institute of Cancer Medicine & Cell Biology
>Locked Bag No.6 Newtown, NSW 2042 AUSTRALIA.
>
>Ph: 61-2-9565-6197 Fax: 61-2-9565-6105
>
>******************************************************
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 http://facsmac.med.cam.ac.uk |
|CB2 |ftp server ftp://131.111.80.78 |
|UK | |
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CD-ROM Vol 3 was produced by Monica M. Shively and other staff at the
Purdue University Cytometry Laboratories and distributed free of charge
as an educational service to the cytometry community.
If you have any comments please direct them to
Dr. J. Paul Robinson, Professor & Director,
PUCL, Purdue University, West Lafayette, IN 47907.
Phone: (765)-494-0757;
FAX(765) 494-0517;
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