Data table header descriptions |
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 |
xDev |
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