| ID_REF | Feature number |
| PositionX | Found X coordinate of feature centroid in pixels |
| PositionY | Found Y coordinate of feature centroid in pixels |
| VALUE | log(REDsignal/GREENsignal) per feature (processed signals used) |
| LogRatioError | error of the log ratio calculated according to the error model chosen |
| PValueLogRatio | Significance level of the Log Ratio computed for a feature |
| gSurrogateUsed | The green surrogate value used |
| rSurrogateUsed | The red surrogate value used |
| gIsFound | A boolean used to flag found (strong) features.The flag is applied independently in each channel. A feature is considered found if the found spot centroid is within the bounds of the spot deviation limit with respect to corresponding nominal centroid. |
| rIsFound | A boolean used to flag found (strong) features.The flag is applied independently in each channel. A feature is considered found if the found spot centroid is within the bounds of the spot deviation limit with respect to corresponding nominal centroid. |
| gProcessedSignal | Dye-normalized signal after surrogate algorithm, green channel, used for computation of log ratio |
| rProcessedSignal | Dye-normalized signal after surrogate algorithm, red channel, used for computation of log ratio |
| gProcessedSigError | Standard error of propagated feature signal, green channel |
| rProcessedSigError | Standard error of propagated feature signal, red channel |
| gNumPixOLHi | Number of outlier pixels per feature with intensity > upper threshold set via the pixel outlier rejection method. The number is computed independently in each channel. These pixels are omitted from all subsequent calculations. |
| rNumPixOLHi | Number of outlier pixels per feature with intensity > upper threshold set via the pixel outlier rejection method. The number is computed independently in each channel. These pixels are omitted from all subsequent calculations. |
| gNumPixOLLo | Number of outlier pixels per feature with intensity < lower threshold set via the pixel outlier rejection method. The number is computed independently in each channel. NOTE: The pixel outlier method is the ONLY step that removes data in Feature Extraction. |
| rNumPixOLLo | Number of outlier pixels per feature with intensity < lower threshold set via the pixel outlier rejection method. The number is computed independently in each channel. NOTE: The pixel outlier method is the ONLY step that removes data in Feature Extraction. |
| gNumPix | Total number of pixels used to compute feature statistics; ie.total number of inlier pixels/per spot; same in both channels |
| rNumPix | Total number of pixels used to compute feature statistics; ie.total number of inlier pixels/per spot; same in both channels |
| gMeanSignal | Raw mean signal of feature in green channel (inlier pixels) |
| rMeanSignal | Raw mean signal of feature in red channel (inlier pixels) |
| gMedianSignal | Raw median signal of feature in green channel (inlier pixels) |
| rMedianSignal | Raw median signal of feature in red channel (inlier pixels) |
| gPixSDev | Standard deviation of all inlier pixels per feature; this is computed independently in each channel |
| rPixSDev | Standard deviation of all inlier pixels per feature; this is computed independently in each channel |
| gBGNumPix | Total Number of pixels used to compute Local BG statistics per spot; ie.total number of BG inlier pixels; same in both channels |
| rBGNumPix | Total Number of pixels used to compute Local BG statistics per spot; ie.total number of BG inlier pixels; same in both channels |
| gBGMeanSignal | Mean local background signal (local to corresponding feature) computed per channel (inlier pixels) |
| rBGMeanSignal | Mean local background signal (local to corresponding feature) computed per channel (inlier pixels) |
| gBGMedianSignal | Median local background signal (local to corresponding feature) computed per channel (inlier pixels) |
| rBGMedianSignal | Median local background signal (local to corresponding feature) computed per channel (inlier pixels) |
| gBGPixSDev | Standard deviation of all inlier pixels per Local BG of each feature, computed independently in each channel |
| rBGPixSDev | Standard deviation of all inlier pixels per Local BG of each feature, computed independently in each channel |
| gNumSatPix | Total number of saturated pixels per feature, computed per channel |
| rNumSatPix | Total number of saturated pixels per feature, computed per channel |
| gIsSaturated | Boolean flag indicating if a feature is saturated or not |
| rIsSaturated | Boolean flag indicating if a feature is saturated or not |
| PixCorrelation | Ratio of estimated feature covariance in RedGreen space to product of feature Standard Deviation in Red Green space. |
| BGPixCorrelation | Ratio of estimated background covariance in RedGreen space to product of background Standard Deviation in Red Green space. |
| gIsFeatNonUnifOL | Boolean flag indicating if a feature is NonUniformity Outlier or not Green Channel |
| rIsFeatNonUnifOL | Boolean flag indicating if a feature is NonUniformity Outlier or not Red Channel |
| gIsBGNonUnifOL | Boolean flag indicating if background is NonUniformity Outlier or not Green Channel |
| rIsBGNonUnifOL | Boolean flag indicating if background is NonUniformity Outlier or not Red Channel |
| gIsFeatPopnOL | Boolean flag indicating if a feature is a Population Outlier or not for Green Channel. Probes with replicate features on a microarray are examined using population statistics |
| rIsFeatPopnOL | Boolean flag indicating if a feature is a Population Outlier or not for Red Channe. Probes with replicate features on a microarray are examined using population statistics |
| gIsBGPopnOL | Boolean flag indicating if background is a Population Outlier or not for Green Channel. |
| rIsBGPopnOL | Boolean flag indicating if background is a Population Outlier or not for Red Channel. |
| IsManualFlag | Manual Flag |
| gBGSubSignal | The net g signal following the subtraction of the background from the raw mean g signal |
| rBGSubSignal | The net r signal following the subtraction of the background from the raw mean r signal |
| gBGSubSigError | Propagated standard error as computed on net g background subtracted signal |
| rBGSubSigError | Propagated standard error as computed on net r background subtracted signal |
| BGSubSigCorrelation | Ratio of estimated background subtracted feature signal covariance in RG space to product of background subtracted feature Standard Deviation in RG space |
| gIsPosAndSignif | Boolean flag indicating if the mean signal of a feature is greater than the corresponding background (selected by user) and if this difference is significant |
| rIsPosAndSignif | Boolean flag indicating if the mean signal of a feature is greater than the corresponding background (selected by user) and if this difference is significant |
| gPValFeatEqBG | P-value from t-test of significance between g Mean signal and g background (selected by user) |
| rPValFeatEqBG | P-value from t-test of significance between r Mean signal and r background (selected by user) |
| gNumBGUsed | Number of local background regions or features used to calculate the background subtraction on this feature g channel. |
| rNumBGUsed | Number of local background regions or features used to calculate the background subtraction on this feature r channel. |
| gIsWellAboveBG | Boolean flag indicating if a feature is WellAbove Background or not |
| rIsWellAboveBG | Boolean flag indicating if a feature is WellAbove Background or not |
| IsUsedBGAdjust | A boolean used to flag features used for computation of global BG offset |
| gBGUsed | Background value (after global background adjust if turned ON) subtracted from the raw mean signal to generate the BG subtracted signal; this value is computed per channel. If global BG subtraction is used the column is identical for every feature in a given channel |
| rBGUsed | Background value (after global background adjust if turned ON) subtracted from the raw mean signal to generate the BG subtracted signal; this value is computed per channel. If global BG subtraction is used the column is identical for every feature in a given channel |
| gBGSDUsed | Standard deviation of background used in g channel |
| rBGSDUsed | Standard deviation of background used in r channel |
| IsNormalization | A boolean flag which indicates if a feature is used to measure dye bias |
| gDyeNormSignal | The dye-normalized signal in the indicated channel |
| rDyeNormSignal | The dye-normalized signal in the indicated channel |
| gDyeNormError | The standard error associated with the dye normalized signal |
| rDyeNormError | The standard error associated with the dye normalized signal |
| DyeNormCorrelation | Dye-normalized red and green pixel correlation |
| ErrorModel | Indicates the error model that you chose for Feature Extraction or that the software uses if you have chosen the “Most Conservative” option |
