Table 2.

Variables stored in the uRNAList object retrieved from the AFE scanned data files.

Variable Name	Description
gMeanSignal	Raw signal.
gProcessedSignal	Signal obtained after all the AFE processing steps (background correction) have been completed. Typically it contains the Multiplicatively Detrended BackgroundSubtracted Signal or the BackgroundSubtractedSignal.
gTotalProbeSignal	Average of all the background corrected signals (gProcessedSignal) for each replicated probe (features with the same sequence) multiplied by the total number of probe replicates.
gTotalGeneSignal	Sum of the TotalProbeSignal over the number of probes per gene.
targets	Contains the name of the AFE scanned data files as specified in the target file.
ProbeName	Agilent-assigned identifier for the probe synthesized on the microarray.
GeneName	Systematic name for the gene for which the probe provides expression information.
ControlType	Specifies whether the feature is a microRNA gene or a control (0 = gene feature, +1 = positive control, -1 = negative control)
gIsGeneDetected	Boolean variable that informs if the gene was detected on the microarray. A feature is considered detected if the signal is three fold greater than the error. If one probe of the probe set for a gene is detected, the gene is considered detected (1 = is detected 0 = is not detected).
gIsSaturated	Boolean flag. 1 indicates that the feature is saturated, i.e. at least half of the inlier pixels in the feature have intensities above the saturation threshold defined by AFE.
gIsFeatNonUnifOL	Boolean flag. 1 indicates that the feature is a non-uniformity outlier; the measured feature pixel variance is greater than the expected feature pixel variance plus the confidence interval.
gIsFeatPopnOL	Boolean flag. 1 indicates that the feature is a population outlier.
gBGMedianSignal	Median raw signal of the local background calculated from intensities of all inlier pixels that represent the local background of the feature.
gBGUsed	Background signal used by AFE algorithms to obtain the background corrected signal. Usually the gBGUsed is the sum of the local background plus the spatial detrending surface value. The spatial detrend surface value estimates the noise due to a systematic gradient on the array.