GPR Metrics Tool Header Overview

• Total Spots: The total number of spots on the array excluding empty spots and control spots
• Missing Spots (%): The number of spots that could not be found during the image quantification process, and as percentage of the total spots in parenthesis
• Bad Spots (%): The number of spots that were manually excluded due to spot saturation or irregular shape, and as a percentage of the total spots in parenthesis
• Useful Spots (%): The number of useful spots used in the quantity assessment and normalization process, and as a percentage of the total spots in parenthesis
• Total Cy5: The total value of the background corrected signal intensity (Mean of signal intensity: Median of background intensity) of all the useful spots for the Cy5 labeled sample in the hybridization
• Total Cy3: The total value of the background corrected signal intensity (Mean of signal intensity: Median of background intensity) of all the useful spots for Cy3 labeled sample in the hybridization
• Ratio (Cy3/Cy5): The ratio of the Total Cy3 over the Total Cy5 of all the useful spots
• Avg. Foreground 635: The average foreground signal intensity (Mean of signal intensity) of all the useful spots for Cy5 labeled sample in the hybridization
• Avg. Foreground 532: The average foreground signal intensity (Mean of signal intensity) of all the useful spots for Cy3 labeled sample in the hybridization
• Avg. Background 635: The average background intensity (Median of background intensity) of all the useful spots for Cy5 labeled sample in the hybridization
• Avg. Background 532: The average background intensity (Median of background intensity) of all the useful spots for Cy3 labeled sample in the hybridization
• Avg. SBR 635: The average of the signal to background value of all the useful spots for the Cy5 labeled sample in the hybridization
• Avg. SBR 532: The average of the signal to background value of all the useful spots for the Cy3 labeled sample in the hybridization
• > 250 Cy5: The number of usable spots with intensity value greater than 250 for the Cy5 labeled channel
• > 250 Cy3: The number of usable spots with intensity value greater than 250 for the Cy3 labeled channel
• > 500 Cy5: The number of usable spots with intensity value greater than 500 for the Cy5 labeled channel
• > 500 Cy3: The number of usable spots with intensity value greater than 500 for the Cy3 labeled channel
• > 1000 Cy5: The number of usable spots with intensity value greater than 1000 for the Cy5 labeled channel
• > 1000 Cy3: The number of usable spots with intensity value greater than 1000 for the Cy3 labeled channel