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 SBQ (stable gene-based quantile normalization) for between-arrays normalization with data from a small-scale array that have a reasonable number of stable genes on it can be downloaded here ("SBQ1_1.pl").

SBQ uses the expression values of stable genes, which are specified in the normalization gene list. It applies quantile normalization to the means of consecutive expression values of stable genes (default is 4 consecutive values) to generate calibration curve for expression values of all the genes on the array. The normalized values of the means of consecutive expression values of stable genes can be saved as an SBQ model. Using the same SBQ model, other array data SBQed separate times can be directly comparable. This is useful when you want to compare many array data. We SBQed many, diverse array data once and saved the model. This "standard" SBQ model is used for all the data newly generated (unless there is any particular reason not to).

The script "SBQ1_1.pl" requires Perl module "Statistics::Regression". Two (or three) input files are needed:
(1) Expression value table file in the tab-delimited text format. The first column is the gene name; the second column is the expression value for sample 1; the third column is the standard error for sample 1; ... and so on. The standard error is actually meaningless, so you can fill the columns for the standard errors with anything.
(2) Normalization gene list, as specified in line 649. These are normalization genes used in SBQ.
(3) Option. If you want to use a normalization model already built by SBQ. The script asks you if you want to use a model.

The script also generates two (or three) output files per run:
(1) Output file: The calculated expression values and standard errors for all the arrays.
(2) Log of the procedure whose name is specified inline 92.
(3) Option. SBQ model: If you choose to export the SBQ model built by the data..