Help by Example for the program GLOG.EXE that finds parameters for the

generalized log transformation using methods from (and similar to)

those from



2003 Sue Geller, Jeff Gregg, Paul Hagerman, and David M. Rocke,

"Transformation and Normalization of Oligonucleotide Microarray Data,"

Bioinformatics, 19, 1817-1823.



There's a sample input file, input.txt, in the same directory as the

executable.  When the executable is run, the default input file is

this file. The program will output the value of c and alpha

(optional). The examples given here are independent,i.e. the settings

aren't carried over to the next example (unmentioned fields are

assumed to be their default values, not the values set in the previous

example).



The transformation parameter is called "c" and the optional estimate

of the background is called "alpha."



Here's a few sample runs of the program:



1) Just click the transform button. (when alpha is checked and robust

   option is set)



c=3800.6

alpha=3.165



2) uncheck alpha, then click the transform button (robust option is

   set).



c=3681.0



3) Uncheck alpha, choose the radio button non-robust, click on

   transform button.



c=9451.6



4) click the advanced button, Select all rows except the first 4 by

   typing 5:n in the "select row" textbox, Select all columns except

   the first by typing 2:n in the "select column" textbox, click on OK

   (which closes Advanced Options dialog), click on transform button

   (when alpha is checked and robust option is set).



c=3909.5

alpha=3.321



5) click the non-robust radio button, click the advanced button, set

   the value of hi to be 20.0, set the value of k to be 3.0, click the

   OK button, click the transform button (alpha is checked).



c=6698.1

alpha=7.974



6) click the advanced button,

   set the value of precision to be 0.0001,

   click on OK,

   click on transform (when robust is set and alpha is checked).



c=3809.5

alpha=3.208



7) click the advanced button, set the value of initial c to be 100,

   set the value of k to be 5, click on OK, click on non-robust radio

   button, uncheck alpha, click on transform button,



c=11300.3



8) when robust option is chosen and alpha is checked, click the

   advanced button, type 100:1000 in the row selection field (there

   are 11952 rows in total), type 2:4 in the column selection field

   (there are 4 columns in total), click on OK, click on transform

   button, an error message appears, saying " Trying to take the log

   of a negative number!"  this error is due to very narrow row

   selection which causes most of the negative elements to be chosen

   from the input file.





Note: when you click on cancel button in Advanced Options Dialog, all

the fields are set to their default values.