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Normalization function was applied to expression data of all experiments and then values of spot replicates within arrays were averaged.
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Then we excluded the outliers and the values of spots replicates within arrays were averaged using a trimmed mean.
Separation of components is shown in Figure 1A and B. The Rf values of spots are given in Table 1.
Namely, the variance values, or σM, for one spot can be pooled, or smoothed, with the σM2 values of spots that are likely to have similar variances.
In contrast, fwhm values of spots in SHaSM images are around 28 nm, about 9 times smaller than the diffraction limit.
Intensity values of spots showing hybridization intensity two standard deviations above background intensity in both channels were used for spot counting and correlation analysis on technical replicates of A. burtoni genomic DNA.
Fluorescence values of spots with maximal intensity (signal saturation) at the chosen laser intensity were extrapolated by linear regression, using values gathered from the two next lower laser intensities.
Each bar represents the normalized and averaged value of spot volume intensity ± standard deviations (SD), obtained by the PDQuest image analysis software.
(There are 20.2 troy pounds of gold in the chest and the price varies every hour. Some of the coins have numismatic value beyond the value of spot gold).
For instance, the maximum value of spot intensity is 65,000 in an Affymetrix scanner.
Mean value of spot volume (dpi) from all three replicate were using to describe the spot density and for further comparison of protein expression, taking into account spots with relative volume equal to or bigger than 0.1 dpi.
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