Oklahoma State University
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GenePix Auto Processor  (GPAP)

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.
GPAP v3.2:
New features
  • Two new background correction methods are available: Robust regression background correction, Edwards no-linear background correction
  • New option for methods of normalization across arrays are available: Scale Normalization, Quantile Normalization and Average Intensity Normalization
  • Dynamically calculate common correlation for within array replicates.
  • User Note: GPAP does not currently have the capability to automate four-color microarray data. Contact us for GPR-file conversion assistance
  • If you have many microarrays to process, contact us for alternative software options.

GPAP v3:

New features:

  • GPAP3 can handle not only Genepix result files (GPR files), but also tab delimited text files with required information, i.e., Block, Row, Column, Unique Identifier, Channel 1 Foreground Mean, Channel 1 Background Median, Channel 2 Foreground Mean, Channel 2 Background Median, and other optional flag information
  • GPAP3 can compare two or more mRNA sources through a common reference mRNA. The files that the user needs to upload are “M and A value for Individual Spot” which can be downloaded after the user finishes processing raw microarray data. Identification of differentially expressed genes can be based on three different statistics, i.e., moderated T-statistics, false discovery controlled P-value and B-statistics
  • GPAP3 has a new normalization implementation for within array normalization method: Loess Normalization on Subset of Control
  • GenesGPAP3 has a support tool to help check the text format microarray data files: to confirm the files contain all required information and are consistent with all biological or technical replicates

    Older versions of GPAP: