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For each channel, the median of the signal intensity and local background values were used.
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Each array was normalized using W303 genomic DNA as reference (Huber et al., 2006), and only transcripts scoring above a threshold background value were used for further processing, as previously published (David et al., 2006).
The parametric-system (PS) method based on background value is used for the quantitative WRV assessment of each subsystem and of the integrated water resources system.
A background value was used to set the threshold between labeled pixels and background pixels.
To evaluate microarray coverage of UHRR, UMRR and URRR on other microarrays, average background intensity values were used as thresholds (either 1X or 2X the background intensity for each channel; Table 3).
These background subtracted values were used for calculating SinR/SigA, SlrR/SigA and SinR / SlrR ratios in Figure 1.
The background-subtracted values were used to calculate the mean G-actin signal in the cytoplasm and a ratio of cortex/cytoplasm ratio for F-actin.
The probe-level background subtracted expression values were used as input for lumi package [ 14] of the R/Bioconductor (http://www.bioconductor.org; http://www.r-project.org) to perform quality control and a quantile normalization.
The background-corrected intensity values were used for analysis.
Duplicate anterior and posterior measurements were made at fixed geometry, and background-corrected geometric mean values were used for clearance curve fitting.
Background subtracted threshold cycle (CT) values were used to determine the absolute quantity of the mRNA based on the standard curve.
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