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For within array and between array normalization, print tip Loess and scale was used.
After each array was normalized within array, the arrays were then normalized across arrays using the A-quantile normalization procedure.
A perchip (within) array normalization was performed using 50 percentile values of all the probe values in the array.
In the first stage the across array fixed effects; panel, dye, treatment and mixed model effects; array and dye within array were modeled.
Inv- inversion within array.
Next, subset-quantile within array normalization (SWAN) was performed.
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Within-array and between-array normalization was performed using loess and scale standardization.
The lowess normalization was done within-array lowess on median of the intensities of the spots.
Lowess normalization was used to normalize the M values for each array separately (within-array normalization).
We combined the within-array replicates on individual arrays and searched for patterns.
After scanning, intensity data were extracted from images, and within-array normalization was accomplished using manufacturer-provided software (NimbleScan).
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