Impatient user's guide to running analyses

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Getting overview results NOW

Login to GALAXY on A6:: (password ZZZZZZ)

At the Huh? prompt, type (ASP, CH, EG, EL, JB, JG, JH, JO, KH, KW, MC, MF, PB, PM, QT, RG, RKH, RUA, SD, SJ, SMR, TE, VE, YW, ZMC etc as appropriate) <return> - this selects your private directory [GALAXY.ASP] (or [GALAXY.KW] etc) where life can be conducted undisturbed. Each private directory has an appropriate logical name, e.g. ASP:

The 'default' overview is BC (type BC <return> to switch back if you have been using others, e.g. CRC, HD etc). To use the 'third frozen' data type BC$ICE3, to use the 'BC 1995' data type BC$KK2, or to use the 'BC 1990' data type BC$KK.

For forest plots need to do 1,2,3 (patient data > intermediate file > graphics); for life table curves, 1,2,4 (same story). Of course, files might already exist from previous graunches. Beware that things go out of date on timescales of hours, as new data and updates are being put in! General remarks: dots are 'placeholders' in parameter lists and usually mean 'nothing'. Filenames as parameters don't need suffices (i.e. don't bother to put filename.DAT).

1. Check the steering file for the relevant treatment comparison; all these are in BC$HB (or BC$HB:*.ICE3, or BC$KK2$HB etc) and are fairly self-explanatory. PLEASE DON'T alter the existing ones!!! If change(s) needed, please copy into a 'clone' and use that. For instance, if you wish to alter BC$HB:TAM12.DAT please copy it to e.g. BC$HB:TAM12EH.DAT and use that.

2. To create the intermediate file containing the annual events, at risk, O-E and Vs:

3a. To produce a forest plot metafile: 3b. To print the forest plot metafile (on GRAFLP): 4a. To produce a life table plot metafile: 4b. To print the life table plot metafile (on GRAFLP): 5. The summary forest plots (one line per stratum) are a two-stage process: 6. The intermediate file for endpoint DDPOSTREC is formed by subtraction between two intermediate files, previously created by BLACKBOX, for the endpoints DD and NONBC. To do this: 94. HELP - most GALAXY things are in HELP. Also, most programs will give you useful information if you give a question mark to them, e.g. BLACK ? There is a document in JG$DK:OVERVIEW.DAT giving fuller details of file locations, software etc.

99. Various explanatory documents attached - lists of file names, purposes and locations; strata and endpoints; definitions of the data processing operations; other programs etc etc. Enjoy!

Changing programs

101. Most GALAXY commands call .EXE programs from the prompt; the sources JG$AK:ABSEIL.FOR, JG$AK:BLACKBOX.FOR and JG$AK:GAZEBO.FOR can easily be cloned and hacked (PLEASE DON'T alter the originals!) For example, PB might create a new PB:XABSEIL.FOR, which can be compiled and linked by typing

What's in GALAXY? - the files

GALAXY is a 'multi-user environment' which contains (amongst other things) overview data and analysis systems for: For each overview, the files held in GALAXY include the following: In many cases there are also 'frozen' versions of the overview data for retrospective analysis.

There are, of course, numerous other files 'off the critical path' including lists of all treatment agents, 'guesses' for missing values of prognostic indicators (not used) and many more experimental things.

The files are all 'flat' human-readable text; however, they conform to certain rules that enable them all to be read by the analysis software too. Techies please note that the 'flat' files are shadowed by sorted binary versions of the information for faster processing - these are automatically regenerated whenever the corresponding 'flat' file is found to have changed.

The analysis software and detailed descriptions of the files can be found via the Contents List, in GALAXY Help and elsewhere.

Checking data NOW

The following remarks are tailored to the BC 2000 and BC 2005 overviews, but apply more or less equally to all of the others.

There are three vital GALAXY programs for data checking:

STARE - finds all the missing items and errors
INQUIST - tabulates all the variables and does statistical tests
LIFE - draws curves
When you have a new file to check, name it BC:##.NEW (where ## is the centre/group number). There are already files BC:##.DAT, which are currently the 'translated' stuff from BC 1995. This doesn't matter, because a .NEW file is given priority over a .DAT file by all the programs.

How to use the programs

Huh? STARE ##
- produces STA##.DAT, a list of all the patient records with problems, with a summary at the end.
STA## is often HUGE and it's usually better just to look at it on the screen. What we used to do was to edit it so that only a manageable number of key problem records remained, and send that to the trialist. (To print it: BURGER STA## H12)
- produces INQ##X1.DAT, a tabulation of all the variables, and INQ##X2.DAT, the statistical tests.
We usually sent INQ##X1 to the trialist. (To print the files: BURGER INQ##X1 H12 or BURGER INQ##X2 H12)
Huh? LIFE #### -1 1
- produces L####V.DAT, a graphics file containing the life-table, accrual and follow-up curves for trial/stratum ####.
(To print the pictures: LASER L####V)
Note: STARE also creates a summary file BC:DBA##.DAT and INQUIST creates BC:DBC##.DAT - these are useful for a quick look, and are used by other programs as data quality indicators and to see how the overview is progressing etc.

There is a fourth program LBASIC which produces the lists of patients with overdue follow-up, missing death causes etc etc, but all this has probably been changed since the last overview.

There are also PC versions of STARE, INQUIST, LIFE, BURGER, LASER, LBASIC etc if required. 

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[End of document, updated to 13 May 2005]