| Data table header descriptions |
| ID_REF |
|
| PositionX |
Found coordinates of the feature centroid in pixels |
| PositionY |
Found coordinates of the feature centroid in pixels |
| VALUE |
(base 10) 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 |
| rIsFound |
A boolean used to flag found (strong) features. The flag is applied independently in each channel |
| gProcessedSignal |
Dye-normalized signal after surrogate algorithm, per channel, used for computation of log ratio |
| rProcessedSignal |
Dye-normalized signal after surrogate algorithm, per channel, used for computation of log ratio |
| gProcessedSigError |
Standard error of propagated feature signal, per channel |
| rProcessedSigError |
Standard error of propagated feature signal, per channel |
| gNumPixOLHi |
Number of outlier pixels per feature with intensity > upper threshold set via the pixel outlier rejection method |
| rNumPixOLHi |
Number of outlier pixels per feature with intensity > upper threshold set via the pixel outlier rejection method |
| gNumPixOLLo |
Number of outlier pixels per feature with intensity < lower threshold set via the pixel outlier rejection method |
| rNumPixOLLo |
Number of outlier pixels per feature with intensity < lower threshold set via the pixel outlier rejection method |
| 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 |
Median local background signal (local to corresponding feature) computed per channel (inlier pixels) |
| rMedianSignal |
Median local background signal (local to corresponding feature) computed per 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. A feature is saturated IF 50% of the pixels in a feature are above the saturation threshold |
| rIsSaturated |
Boolean flag indicating if a feature is saturated or not. A feature is saturated IF 50% of the pixels in a feature are above the saturation threshold |
| PixCorrelation |
Ratio of estimated feature covariance in RedGreen space to product of feature Standard Deviation in Red Green space |
| BGPixCorrelation |
The same concept as above but in case of background |
| gIsFeatNonUnifOL |
Boolean flag indicating if a feature is a NonUniformity Outlier or not. A feature is non-uniform if the pixel noise of feature exceeds a threshold established for a "uniform" feature |
| rIsFeatNonUnifOL |
Boolean flag indicating if a feature is a NonUniformity Outlier or not. A feature is non-uniform if the pixel noise of feature exceeds a threshold established for a "uniform" feature |
| gIsBGNonUnifOL |
The same concept as above but in case of background |
| rIsBGNonUnifOL |
The same concept as above but in case of background |
| gIsFeatPopnOL |
Boolean flag indicating if a feature is a Population Outlier or not. 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. Probes with replicate features on a microarray are examined using population statistics |
| gIsBGPopnOL |
The same concept as above but in case of background |
| rIsBGPopnOL |
The same concept as above but in case of background |
| IsManualFlag |
Boolean is manual flag |
| gBGSubSignal |
Background-subtracted signal |
| rBGSubSignal |
Background-subtracted signal |
| gBGSubSigError |
Propagated standard error as computed on net g(r) background subtracted signal |
| rBGSubSigError |
Propagated standard error as computed on net g(r) background subtracted signal |
| BGSubSigCorrelation |
Ratio of estimated background-subtracted feature signal co-variance in RG space to product of background-subtracted feature Standard Deviation in RG space |
| gIsPosAndSignif |
Boolean flag, established via a 2-sided t-test, indicates 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, established via a 2-sided t-test, indicates 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(r) Mean signal and g(r) background (selected by user) |
| rPValFeatEqBG |
P-value from t-test of significance between g(r) Mean signal and g(r) background (selected by user) |
| gNumBGUsed |
Background used to subtract from the MeanSignal; variable also used in t-test |
| rNumBGUsed |
Background used to subtract from the MeanSignal; variable also used in t-test |
| 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 |
Boolean used to flag features used for computation of global BG offset |
| gBGUsed |
Background used to subtract fromthe MeanSignal; variable also used in t-test |
| rBGUsed |
Background used to subtract fromthe MeanSignal; variable also used in t-test |
| gBGSDUsed |
Standard deviation of background used in g(r) channel; variable also used in t-test and surrogate algorithms |
| rBGSDUsed |
Standard deviation of background used in g(r) channel; variable also used in t-test and surrogate algorithms |
| IsNormalization |
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 |
