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OFRG
Macro Page of OFRG
Excel Macros

BRIEF INTRODUCTION


Various excel macros are provided to facilitate raw data analysis. They extract signals from microarray images, binarize intensity values, and generate theoretical fingerprints. These macros are developed with Microsoft Excel. Please download the Excel files and follow the directions in the readme sheets therein. Here is the overview of the OFRG data analysis.


GENE ID GENERATOR

Gene ID Generator serves as a supplement to the Imagene software. It assigns a unique ID to each clone by concatenating the treatment plate number and the information of meta row and meta column of the clone. The gene ID will be used to trace the position of the clone. User's Guide


BACKGROUND SUBTRACTION

Background Subtraction is used to fetch all valid hybridization signals (i.e., not flagged as 2) from the Imagene's output by removing the background. The processed data will be used to generate normalized signals and binarized fingerprints eventually. User's Guide


FLAG COLUMN TOOL

Flag Column Tool is specially provided to expunge missing or negative spots (i.e., flagged as 2) for reference probes in any one of the four replicate hybridizations from the Imagene output. User's Guide


FINGERPRINT ASSIGNMENT

Fingerprint Assignment Tool is the key component among the macros. Here, the hybridization signals with background subtracted are first normalized by dividing the signal value of the hybridization between each clone and each probe by that of the hybrization between the same clone and the reference probe. Next the hybridization result of a clone with a set of probes will be converted to a binary fingerprint, which is calculated by comparing their normalized signals with those of control clones. Gaussian models are adopted to assign binary fingerprints with subjective threshold values. User's Guide


THEORETICAL FINGERPRINT GENERATOR

Theoretical fingerprint generator will generate theoretical fingerprint for each rDNA sequence in a file and probe set file, with 0 being assigned if the sequence contains probe and 1 assigned otherwise. Theoretical fingerprints are useful in probe set design and the calculation of the discriminating ratio of OFRG methods. User's Guide


STATISTICAL ANALYSIS

Statistical anylyses such as ANOVA, stepwise regression analysis and discriminant analysis etc are conducted using SAS v.8.02 (SAS Institute, Inc. Cary NC 27153) programs. Detailed user guide for these statistical analysis can be found here.


ONE PROBE ANALYSIS TOOL

One Probe Analysis Tool is a simple spreadsheet that can be used with one probe at a time to assign fingerprints to signal intensities. It uses a fixed boundary version of the modified Bayes rules that are used in the Fingerprint Assignment Tool. The rules in the latter file are more advanced and we recommend using them to assign fingerprints.User's Guide


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Copyright @ by Oligonucleotide Fingerprinting of Ribosomal RNA Genes(OFRG) Group (zliu@cs.ucr.edu, qfu@cs.ucr.edu), 2002

Last Modified on 04/25/2013