Data table header descriptions |
ID_REF |
ID_REF |
RAW.G_MEAN_SIGNAL |
Mean foreground intensity Ch 1.; Type: float; Scale: linear_scale |
RAW.G_MEDIAN_SIGNAL |
Median foreground intensity Ch 1.; Type: float; Scale: linear_scale |
RAW.R_MEAN_SIGNAL |
Mean foreground intensity Ch 2.; Type: float; Scale: linear_scale |
RAW.R_MEDIAN_SIGNAL |
Median foreground intensity Ch 2.; Type: float; Scale: linear_scale |
RAW.G_MEAN_BG |
Mean background intensity Ch 1.; Type: float; Scale: linear_scale; Background |
RAW.G_MEDIAN_BG |
Median background intensity Ch 1.; Type: float; Scale: linear_scale; Background |
RAW.R_MEAN_BG |
Mean background intensity Ch 2.; Type: float; Scale: linear_scale; Background |
RAW.R_MEDIAN_BG |
Median background intensity Ch 2.; Type: float; Scale: linear_scale; Background |
RAW.G_NUM_PIX |
Total number of pixels used to compute feature statistics; ie. Total number of inlier pixels per spot, computed independently for the green channel. The number of inlier pixels are the same in both channels.; Type: integer; Scale: linear_scale |
RAW.R_NUM_PIX |
Total number of pixels used to compute feature statistics; ie. Total number of inlier pixels per spot, computed independently for the red channel. The number of inlier pixels are the same in both channels.; Type: integer; Scale: linear_scale |
RAW.G_PIX_SDEV |
Standard deviation of all inlier pixels per feature; this is computed independently for the green channel; Type: float; Scale: linear_scale |
RAW.R_PIX_SDEV |
Standard deviation of all inlier pixels per feature; this is computed independently for the red channel; Type: float; Scale: linear_scale |
RAW.G_BG_NUM_PIX |
Total number of pixels used to compute Local background statistics per spot; ie. Total number of BG inlier pixels. This number is calculated independently for the green channel.; Type: integer; Scale: linear_scale |
RAW.R_BG_NUM_PIX |
Total number of pixels used to compute Local background statistics per spot; ie. Total number of BG inlier pixels. This number is calculated independently for the red channel.; Type: integer; Scale: linear_scale |
RAW.G_BG_PIX_SDEV |
Standard deviation of all inlier pixels per feature; this is computed independently for the green channel; Type: float; Scale: linear_scale |
RAW.R_BG_PIX_SDEV |
Standard deviation of all inlier pixels per feature; this is computed independently for the red channel; Type: float; Scale: linear_scale |
RAW.TOP |
Top coordinate of "box" containing spot in gif image; Type: integer; Scale: linear_scale |
RAW.BOT |
Bottom coordinate of "box" containing spot in gif image; Type: integer; Scale: linear_scale |
RAW.LEFT |
Left coordinate of "box" containing spot in gif image; Type: integer; Scale: linear_scale |
RAW.RIGHT |
Right coordinate of "box" containing spot in gif image; Type: integer; Scale: linear_scale |
RAW.POSITION_X |
X-coordinate of spot.; Type: float; Scale: linear_scale |
RAW.POSITION_Y |
Y-coordinate of spot.; Type: float; Scale: linear_scale |
COMPUTED.BG_PIX_CORRELATION |
Ratio of estimated feature Background covariance in Red Green space to product of feature Standard Deviation in Red Green space. The covariance of two features measures their tendency to vary together, ie., co-vary. In this case, it is a cumulative quantitation of the tendency of pixels belonging to a particular feature's Background in Red and Green spaces to co-vary.; Type: float; Scale: linear_scale |
COMPUTED.BG_SUB_SIG_CORRELATION |
Ratio of estimated background subtracted feature signal covariance in Red Green space to product of background subtracted feature Standard Deviation in Red Green space.; Type: float; Scale: linear_scale |
COMPUTED.G_BG_SD_USED |
Standard deviation of background used in green channel; Type: float; Scale: linear_scale; Background |
COMPUTED.G_BG_SUB_SIGNAL |
The net green signal following the subtraction of the background from the raw green mean signal; Type: float; Scale: linear_scale |
COMPUTED.G_BG_SUB_SIG_ERROR |
Propagated standard error as computed on net green background subtracted signal; Type: float; Scale: linear_scale |
COMPUTED.G_BG_USED |
Background value subtracted from the raw mean signal to generate the BG subtracted signal; this value is computed for the green channel. If global BG subtraction is used, the column is identical for every feature in a channel. Options: gBGSubSignal (gMeansignal - gBGUsed); Type: float; Scale: linear_scale |
COMPUTED.R_BG_SD_USED |
Standard deviation of background used in red channel; Type: float; Scale: linear_scale; Background |
COMPUTED.R_BG_SUB_SIGNAL |
The net green signal following the subtraction of the background from the raw red mean signal; Type: float; Scale: linear_scale |
COMPUTED.R_BG_SUB_SIG_ERROR |
Propagated standard error as computed on net red background subtracted signal; Type: float; Scale: linear_scale |
COMPUTED.R_BG_USED |
Background value subtracted from the raw mean signal to generate the BG subtracted signal; this value is computed for the red channel. If global BG subtraction is used, the column is identical for every feature in a channel. Options: rBGSubSignal (rMeansignal - rBGUsed); Type: float; Scale: linear_scale |
COMPUTED.G_DYE_NORM_SIGNAL |
The dye normalized signal in the green channel.; Type: float; Scale: linear_scale |
COMPUTED.R_DYE_NORM_SIGNAL |
The dye normalized signal in the red channel.; Type: float; Scale: linear_scale |
COMPUTED.G_IS_GOOD_PM |
Feature passes gIsWellAboveBG and additionally the gPerfMatchSignal is positive and significant (t-test p value < 0.01) versus its gDelCtrlSignal; Type: float; Scale: linear_scale |
COMPUTED.G_IS_LOW_SPECIFICITY |
gPerfMatchSignal fails positive and significance t-test (0.01) versus its gDelCtrlSignal; and deletion control passes gIsWellAboveBG; Type: float; Scale: linear_scale |
COMPUTED.R_IS_GOOD_PM |
Feature passes rIsWellAboveBG and additionally the rPerfMatchSignal is positive and significant (t-test p value < 0.01) versus its rDelCtrlSignal; Type: float; Scale: linear_scale |
COMPUTED.R_IS_LOW_SPECIFICITY |
rPerfMatchSignal fails positive and significance t-test (0.01) versus its rDelCtrlSignal; and deletion control passes rIsWellAboveBG; Type: float; Scale: linear_scale |
COMPUTED.G_NUM_SAT_PIX |
Total number of saturated pixels per feature, computed for the green channel; Type: integer; Scale: linear_scale |
COMPUTED.R_NUM_SAT_PIX |
Total number of saturated pixels per feature, computed for the red channel; Type: integer; Scale: linear_scale |
COMPUTED.G_PROCESSED_SIGNAL |
The propagated feature signal in the green channel, used for computation of log ratio; Type: float; Scale: linear_scale |
COMPUTED.R_PROCESSED_SIGNAL |
The propagated feature signal in the red channel, used for computation of log ratio; Type: float; Scale: linear_scale |
COMPUTED.G_PVAL_FEAT_EQ_BG |
Log (base 10) of p-value from t-test of significance between green Mean signal and green background.; Type: float; Scale: linear_scale |
COMPUTED.R_PVAL_FEAT_EQ_BG |
Log (base 10) of p-value from t-test of significance between red Mean signal and red background.; Type: float; Scale: linear_scale |
VALUE |
log10(REDsignal/GREENsignal); Type: float; Scale: linear_scale |
COMPUTED.LOG_RATIO_ERROR |
Error of the log ratio calculated according to the error model chosen.; Type: float; Scale: linear_scale |
COMPUTED.PIX_CORRELATION |
Ratio of estimated feature covariance in Red Green space to product of feature Standard Deviation ion Red Green space. The covariance of two features measures their tendency to vary together, ie., co-vary. In this case, it is a cumultive quantitation of the tendency of pixels belonging to a particular feature in Red and Green spaces to co-vary.; Type: float; Scale: linear_scale |
COMPUTED.P_VALUE_LOG_RATIO |
Log (base 10) of significance level of the Log Ratio computed for a feature.; Type: float; Scale: linear_scale |
COMPUTED.DYE_NORM_CORRELATION |
Dye normalized red and green pixel correlation.; Type: float; Scale: linear_scale |
COMPUTED.G_DYE_NORM_ERROR |
The standard error associated with the green dye normalized signal.; Type: float; Scale: linear_scale |
COMPUTED.R_DYE_NORM_ERROR |
The standard error associated with the red dye normalized signal.; Type: float; Scale: linear_scale |
COMPUTED.ERROR_MODEL |
Indicates the error model that the user chose for feature extraction. Options: 0 (Propagated model chosen by user or by software) | 1 (Universal error model chosen by user of software).; Type: integer; Scale: linear_scale |
COMPUTED.G_IS_FOUND |
A boolean used to flag found (strong) features. The flag is applied independently to the green 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. NOTE: Isfound was previously termed IsStrong.; Type: boolean; Scale: linear_scale |
COMPUTED.R_IS_FOUND |
A boolean used to flag found (strong) features. The flag is applied independently to the red 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. NOTE: Isfound was previously termed IsStrong.; Type: boolean; Scale: linear_scale |
COMPUTED.G_IS_FEAT_NON_UNIF_OL |
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. Option 1 (Feature is a non-uniformity outlier in the green channel).; Type: boolean; Scale: linear_scale |
COMPUTED.R_IS_FEAT_NON_UNIF_OL |
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. Option 1 (Feature is a non-uniformity outlier in the red channel).; Type: boolean; Scale: linear_scale |
COMPUTED.G_IS_FEAT_POPN_OL |
Boolean flag indicating if a feature is a Population Outlier or not. Probes with replicate features on a microarray are examined using population statistics. A feature is a population outlier if its signal is less than a lower threshold or exceeds an upper threshold determined using the interquartile range (ie., IQR) of the population. Options: 1 (feature is a population outlier in the green channel).; Type: boolean; Scale: linear_scale |
COMPUTED.R_IS_FEAT_POPN_OL |
Boolean flag indicating if a feature is a Population Outlier or not. Probes with replicate features on a microarray are examined using population statistics. A feature is a population outlier if its signal is less than a lower threshold or exceeds an upper threshold determined using the interquartile range (ie., IQR) of the population. Options: 1 (feature is a population outlier in the red channel).; Type: boolean; Scale: linear_scale |
COMPUTED.G_IS_SATURATED |
Boolean flag indicating if a feature is saturated or not in the green channel. A feature is saturated IF 50% of the pixels in a feature are above the saturation threshold. Options: 1 (saturated) | 0 (not saturated); Type: boolean; Scale: linear_scale |
COMPUTED.R_IS_SATURATED |
Boolean flag indicating if a feature is saturated or not in the red channel. A feature is saturated IF 50% of the pixels in a feature are above the saturation threshold. Options: 1 (saturated) | 0 (not saturated); Type: boolean; Scale: linear_scale |
COMPUTED.R_IS_WELL_ABOVE_BG |
Boolean flag indicating if a feature is well above background or not. Feature passes if RIsPosAndSignif AND RBGSubSignal is greater than 2.6*RBG_SD.Boolean flag indicating if a feature is well above background or not. Feature passes if RIsPosAndSignif AND RBGSubSignal is greater than 2.6*RBG_SD.; Type: boolean; Scale: linear_scale |
COMPUTED.G_IS_WELL_ABOVE_BG |
Boolean flag indicating if a feature is well above background or not. Feature passes if RIsPosAndSignif AND RBGSubSignal is greater than 2.6*RBG_SD.Boolean flag indicating if a feature is well above background or not. Feature passes if RIsPosAndSignif AND RBGSubSignal is greater than 2.6*RBG_SD.; Type: boolean; Scale: linear_scale |
COMPUTED.G_IS_BG_NON_UNIF_OL |
Boolean flag indicating if a feature's Background 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. Option 1 (Feature's background is a non-uniformity outlier in the green channel).; Type: boolean; Scale: linear_scale |
COMPUTED.R_IS_BG_NON_UNIF_OL |
Boolean flag indicating if a feature's Background 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. Option 1 (Feature's background is a non-uniformity outlier in the red channel).; Type: boolean; Scale: linear_scale |
COMPUTED.G_IS_BG_POPN_OL |
Boolean flag indicating if a feature's Background is a Population Outlier or not. Probes with replicate features on a microarray are examined using population statistics. A feature's background is a population outlier if its signal is less than a lower threshold or exceeds an upper threshold determined using the interquartile range (ie., IQR) of the population. Options: 1 (feature Background is a population outlier in the green channel).; Type: boolean; Scale: linear_scale |
COMPUTED.R_IS_BG_POPN_OL |
Boolean flag indicating if a feature's Background is a Population Outlier or not. Probes with replicate features on a microarray are examined using population statistics. A feature's background is a population outlier if its signal is less than a lower threshold or exceeds an upper threshold determined using the interquartile range (ie., IQR) of the population. Options: 1 (feature Background is a population outlier in the red channel).; Type: boolean; Scale: linear_scale |
COMPUTED.G_IS_POS_AND_SIGNIF |
Boolean flag indicating if the mean signal of a feature is greater than the corresponding background and if this difference is significant. Significance is established via a 2-sided t-test against the user-settable maximum p-value (BGSub tab) Options: 1 (Feature is positive and significant above background in the green channel); Type: boolean; Scale: linear_scale |
COMPUTED.R_IS_POS_AND_SIGNIF |
Boolean flag indicating if the mean signal of a feature is greater than the corresponding background and if this difference is significant. Significance is established via a 2-sided t-test against the user-settable maximum p-value (BGSub tab) Options: 1 (Feature is positive and significant above background in the red channel); Type: boolean; Scale: linear_scale |
COMPUTED.IS_USED_BG_ADJUST |
Boolean flag used to flag features used for computation of global Background offset; Type: boolean; Scale: linear_scale |
COMPUTED.IS_NORMALIZATION |
Boolean flag which indicates if a feaure is used to measure dye bias. Options: 1 (Feature used) | 0 (Feature not used).; Type: boolean; Scale: linear_scale |