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Raw data were converted into cluster presence or absence by applying an expression threshold (set to 1.5X the median background value using a log2 scale).
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Raf specific titers were compared to the background values using a two tailed Mann-Whitney U test with a 95% confidence interval.
For comparison, we also compute the PVE corrected mean value using a global background for each ROI (see below).
For this study, the background values used were the averages of those from SE5000 and the reference station.
The average background value was calculated using a subset of 1000 non-expressed genes found in the whole CATMA database.
Options such as not correcting for background, using a global background value for every spot, or using negative control values as a background can be successful in some cases, but are not robust.
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).
Measured fluorescence polarization values were converted into anisotropy (FA) values and subsequently background-subtracted using a no-ORC1 5 no-ORC1 5eacontrolyields ΔFA).
These situations can be rectified in arbitrary ways; for instance, by setting backgrounds to a non-zero value and using a logarithm transform of the ratio.
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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