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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.
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A background value was used to set the threshold between labeled pixels and background pixels.
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).
For each channel, the median of the signal intensity and local background values were used.
DOI: http://dx.doi.org/10.7554/eLife.11611.025 Two threshold values are specified interactively with a slider: the lower value is used to separate cells from the background and the higher value is used to define polarity spots within the cells.
Each spot of the array membrane was quantified by the image analysis software UN-Scan-It (Silk Scientific, Orem, UT, USA) in triplicate with background correction and the mean value was used.
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.
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