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GenePix Auto Processor(GPAP) is designed to assist with preprocessing of raw microarray data and provides diagnostic plots to evaluate the data quality and effects of preprocessing. GPAP will perform signal filtering, background correction and signal normalization. GPAP will generate reports, diagnostic plots and identify top differentially expressed genes for the user.
File names for GAL file and GPR files must start with a letter and should be less than 20 characters.  All GPR files should have the same number of features and the same layout as GAL file. Please review the GPAP upload check-list to avoid processing errors caused by improper file names and format.

Update: Please note that GAL files are no longer required for GPAP processing of GPR files. To correctly coordinate replicate spots between GPR files, please verify that all of your GRP files are sorted in exactly the same way (e.g., first by block, then row, then column). Please review the GPAP upload check-list to avoid processing errors caused by improper file names and format.

Fields marked with an * are required. A minimum of two GPR files with different names (biological and/or technical reps) is required for processing. Please review the checklist for further details.

Replicate mapping for B-statistic ranking:
Applies only if reps are printed at regular intervals between replicate arrays and not within arrays
Number of replicates on the microarray =
Number of spots separating each replicate =
Unique Identifier: Name   ID  

Each GPR below must be biological or technical replicates of the same single treatment or timepoint.
1st GPR:  *  Dye Swap(Cy3/Cy5): 
2nd GPR:  *  Dye Swap(Cy3/Cy5): 
3rd GPR:  Dye Swap(Cy3/Cy5): 
4th GPR:  Dye Swap(Cy3/Cy5): 
5th GPR:  Dye Swap(Cy3/Cy5): 
6th GPR:  Dye Swap(Cy3/Cy5): 
*Required
Note: Click the Browse button to upload your GPR files. It is assumed each GPR file use the same wavelengths for Cy5 and Cy3
Baseline Value:
Note: If signal in one channel falls below this baseline, the signal in that channel will be increased to this value. If in both channels, that feature will be discarded.
Parameter for Threshold Value:  x=
Note: Threshold Value = B + x*SD(B) (x=1,2,3) If signal in one channel falls below this threshold value, the signal in that channel will be increased to baseline value. If in both channels, that feature will be discarded.
Parameter for Outliers Definition: x=
Note: Outlier > mean + x*SD or Outlier < mean - x*SD (x=1,2,3). For those replicate spots which are greater or lower than 2(default value) standard deviations from mean  are defined to be outliers and are eliminated from calculation when average is calculated for each gene.
Normalization:

  
 

This facility is part of the OSU Recombinant DNA/Protein Resource Core Facility housed the Noble Research Center within the Department of Biochemistry and Molecular Biology.
 
349 Noble Research Center
Stillwater, OK 74078
Patricia Ayoubi, PhD
Phone: 405-744-6209 (O)
Phone: 405-744-6817 (L)
 
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