The software listed in this site is for non-commercial use only. It is provided as is, and it comes with no guaranttee. Neither current and former members of Glazebrook and Katagiri Labs nor Univ. of Minnesota are responsible for any damage caused by use of the software.

Perl script for calculating the expression values from the fluorescence value for each spot on the array (in .gpr, output from GenePix) can be down loaded here ("Cy3_auto_ExpValCal_SBQ1_3_2.pl").

The script "Cy3_auto_ExpValCal_SBQ1_3_2.pl" requires Perl module "Statistics::Regression" and R (http://www.r-project.org/;the script is written for ver. 2.3.1). According to where R.exe is in your computer, the R_path (line 33) needs to be modified. Two (or three) kinds of input files are needed:
(1) Fluorescence value data files in .gpr format (GenePix). The script is written so that it processes all the .gpr file in the current working directory. For each array, two .gpr files with different laser powers ("low" and "high") in scanning are needed. When all the .gpr file names in the directory is alphabetically sorted, each pair of low and high file names have to become consecutive and the low file name has to come before the high file name for each pair.
(2) Normalization gene list, as specified in line 649. These are normalization genes used in SBQ. See an SBQ description here.
(3) Option. If you want to use a normalization model already built by SBQ, the normalization model. The script asks you if you want to use a model.

The script generates three output files for each array (i.e., every pair of "low" and "high" .gpr files):
(1) "_OtherInfo.txt": Records of invalid spot data, fitted model parameters for each spot, etc.
(2) "_combCy3.txt": Spot-by-spot fluorescence values calculated by combining "low" and "high" data.
(3) "_ExpVal.txt": Calculated expression values and standard errors.
(4) "_Rsum.txt": Summary of the linear model fit in R

The script also generates additional two (or three) output files per run:
(1) "_SBQed.txt": The calculated expression values and standard errors for all the arrays.
(2) Log of the procedure whose name is specified inline 45.
(3) Option "_SBQmodel.txt": If you choose to export the SBQ model built by the data, it gets saved.

Some other files are generated for the purpose of communicating between Perl and R, but you can ignore them.