Getting modal values and ASCII listings on Consort/VAX systems

Robert F. Murphy (MURPHY@A.CFR.CMU.EDU)
Wed, 19 Aug 1992 15:39:04 EDT

In response to a question from Ray Hester (as discussed by Alice Givan,
Eric van Buren and Mike Lance), there are at least three ways to find
mode values for FCS files on Consort/VAX systems.

1. Use the GI command in DISP4 followed by the H command (after
positioning the cursor in a particular histogram).

2. Read the file into COTFIT using the INPUT command, specify which
parameter you want to read, use the DELETE command to remove the
cell-cycling function which is automatically assumed for FCS files,
and then use the FIT command to get a listing of statistics. The
mode is found after the words "Y Peak at X=".

3. For files acquired with ACQ8 V5.3, the PKn keywords contain the mode
for each parameter. There are three of these keywords for each
parameter: PKnT contains the mode for the entire histogram of parameter
n, PKnWL contains the mode for the portion of the histogram within
the left window, and PKnWR contains the mode for the portion in the
right window.

As for generating ASCII files, Eric van Buren correctly points out that
the PS command can be used. You can write the listing to a file by
setting the logical name LP to point to a disk before you enter DISP4.
For example:

$ ASSIGN listing.ascii LP
$ DISP4

Each time the PS command is given, a new file with the assigned name
will be created.

An alternative is to use the FCSLST program (this is the program
mentioned by Alice Givan). It will generate an ASCII file from any FCS
1.0 file (list mode, single paramter histograms, dual parameter
histograms). It is available from CMU via anonymous FTP
(address: a.cfr.cmu.edu, directory: [.VMS.FCSLST], file FCSLST.EXE).

Bob Murphy


Home Page Table of Contents Sponsors Web Sites
CD ROM Vol 2 was produced by 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:(317) 494-0757; FAX (317) 494-0517; Web http://www.cyto.purdue.edu EMAIL robinson@flowcyt.cyto.purdue.edu