Bonferroni correction was implemented for post-hoc comparison.
A reaction-field correction was used for long-range electrostatic interactions, and an energy dispersion correction was implemented.
In the second step correction is implemented for these detectors.
This correction is implemented throughout.
The correction is implemented using resampling as before.
Unweighted multiple testing corrections were implemented for these two tests.
For mouse arrays, background correction was performed using the 'normexp' method implemented in the Bioconductor LIMMA package to adjust local median background estimates (54).
Microarray data were analyzed using the software package limma (Linear Models for Microarray Data) [ 56] implemented in R. Background correction was done using the subtract method and within array normalization was performed with the loess method [ 57].
Background correction was performed with the model-based procedure [ 18] using sequence information as implemented in the Bioconductor package gcrma.
Background correction was made using a reference blank KBr pellet.
