PUMAdb : Note on Agilent Data Formats

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Description

Beginning in version 10.5 of the Agilent Feature Extraction software, the default output format is "compact" which cuts the file size (of the .txt file) by about half. Where the "full" output contains 114 FEATURE attributes, the "compact" only contains 42. If you load experiments in "compact" version, be aware that you can only filter by the fields that the compact format supports. (We do not require nor even recommend that you use the "compact" format. File size is not an issue for PUMA. To change the setting in the Feature Extraction software, click the project properties, and select full in the FeatureExtractor output package box.)

Lists of Fields

Fields included in both the full and compact formats:
  • Green Net Intensity
  • Feature Is Green Background Non-uniformity Outlier (0|1)
  • Feature Is Green Background Population Outlier (0|1)
  • Feature Is Green Non-uniformity Outlier (0|1)
  • Feature Is Green Population Outlier (0|1)
  • Green Net Intensity Is Positive and Significant (0|1)
  • Green Channel Saturated (0|1)
  • Green Intensity Is Well Above Background (0|1)
  • Final Processed Green Intensity
  • GProcessedSigError
  • log(base 10) (REDsignal/GREENsignal)
  • Error of Log Ratio
  • log(base 10) (P-value of Log Ratio)
  • Red Net Intensity
  • Feature Is Red Background Non-uniformity Outlier (0|1)
  • Feature Is Red Background Population Outlier (0|1)
  • Feature Is Red Non-uniformity Outlier (0|1)
  • Feature Is Red Population Outlier (0|1)
  • Red Net Intensity Is Positive and Significant (0|1)
  • Red Channel Saturated (0|1)
  • Red Intensity Is Well Above Background (0|1)
  • Final Processed Red Intensity
  • RProcessedSigError
  • Feature
  • Standard Deviation of Green Background Inlier Pixels
  • Green Background (mean)
  • Green Background (median)
  • Green Intensity (median)
  • X coordinate
  • Y coordinate
  • Standard Deviation of Red Background Inlier Pixels
  • Red Background (mean)
  • Red Background (median)
  • Red Intensity (median)
 Fields included only in the full format:
  • Background Pixel Correlation
  • Red-Green Net Pixel Correlation
  • Red-Green Normalized Net Pixel Correlation
  • Error Model Used (0|1)
  • Std Dev of Green Background Intensity
  • Std Err of Green Net Intensity
  • Green Background Intensity Used
  • Green Intensity Error of Corresponding Deletion Control
  • Green Mean Intensity of Corresponding Deletion Control
  • Std Err of Green Normalized Net Intensity
  • Green Normalized Net Intensity
  • GHighEndCorrDNError
  • GHighEndCorrDNSig
  • Feature Is Found (Green) (0|1)
  • PM Is Strong and Significant vs DC (Green) (0|1)
  • PM Is Low Specificity vs DC (Green) (0|1)
  • GNumBGUsed
  • Number of Green Outlier Pixels (high intensity)
  • Number of Green Outlier Pixels (low intensity)
  • Number of Green Saturated Pixels
  • Green Intensity Error of Perfect Match
  • Green Mean Intensity of Perfect Match
  • log(base 10) (Ratio of Green Mean PM Intensity to DC Intensity)
  • log(base 10) (P-value of Green Difference from Background)
  • log(base 10) (P-value of Green PM/DC Difference)
  • Green Surrogate Used
  • HighEndCorrDNCorrelation
  • HighEndDyeNormApplied (0|1)
  • Feature Is Used for Normalization (0|1)
  • Feature Is Used for Global Background (0|1)
  • Red-Green Pixel Correlation
  • Std Dev of Red Background Intensity
  • Std Err of Red Net Intensity
  • Red Background Intensity Used
  • Red Intensity Error of Corresponding Deletion Control
  • Red Mean Intensity of Corresponding Deletion Control
  • Std Err of Red Normalized Net Intensity
  • Red Normalized Net Intensity
  • RHighEndCorrDNError
  • RHighEndCorrDNSig
  • Feature Is Found (Red) (0|1)
  • PM Is Strong and Significant vs DC (Red) (0|1)
  • PM Is Low Specificity vs DC (Red) (0|1)
  • RNumBGUsed
  • Number of Red Outlier Pixels (high intensity)
  • Number of Red Outlier Pixels (low intensity)
  • Number of Red Saturated Pixels
  • Red Intensity Error of Perfect Match
  • Red Mean Intensity of Perfect Match
  • log(base 10) (Ratio of Red Mean PM Intensity to DC Intensity)
  • log(base 10) (P-value of Red Difference from Background)
  • log(base 10) (P-value of Red PM/DC Difference)
  • Red Surrogate Used
  • Manual Flag
  • Number of Green Background Pixels
  • Green Intensity (mean)
  • Number of Green Inlier Pixels
  • Standard Deviation of Green Inlier Pixels
  • Number of Red Background Pixels
  • Red Intensity (mean)
  • Number of Red Inlier Pixels
  • Standard Deviation of Red Inlier Pixels