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Median foreground pixel intensities for spots were adjusted by subtracting median background pixel intensities.
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Signal intensities were measured according to the local background subtraction method as a function of the median of foreground pixels minus median of background pixels.
Signal intensities were measured according to the local background subtraction method as a function of the median of foreground pixels minus the median of background pixels.
The gene expression ratios are calculated as the median value of the pixels minus background pixel median value for one color channel divided by those for the other channel.
Background levels were calculated locally for each spot using the median of the background pixels.
Bands of interest were manually selected and their total intensity quantified with subtraction of median background signal from an area 3-pixels wide above and below the band in the same lane.
The BSI, calculated by subtracting median background from total intensity divided by the number of pixels in feature, was used in the following statistical data analysis.
This involved selecting spots detected on at least half of the microarrays with at least 70% pixels above threshold intensity (set to the median background plus two standard deviations).
Information extraction for a given spot is based on the median value for the signal pixels minus the median value for the background pixels to produce a gene set data file for all the DNA spots.
The total fluorescence intensity of each object was determined by integrating the intensities of all pixels associated with the object and subtracting the local median background intensity.
Only spots detected with at least 70% of their pixels above the threshold intensity signal (set to the median background plus two standard deviations) were selected.
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