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For overexpressed genes in the surgical or biopsy samples, we first selected genes by u-test (p<0.01), permutation test, and 2- or 3-fold change between the average signal intensities of the two sets of samples, and from the first selected genes we finally selected genes with more than 1,000 in average signal intensity.
In fact, no correlation is found between the average signal intensity of LTR sequences and the average of the nearest gene (Additional file 2; Figure S2).
Highly expressed genes that showed greater than a two-fold difference between the average signal values of the control and test groups were selected for further study.
Comparing different groups, a "fold change" (FC) was calculated, which is the ratio between the average signal values of groups to be compared.
The optimum threshold is obtained in a way that maximizes the distance between the average signal intensities of the initially segmented neuron region and its background.
The Diff Score is a transformation of the P-value that provides directionality to the P-value based on the difference between the average signal in the reference group versus the comparison group.
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Also, unlike traditional normalization processing, SDOS is used and the mapping between SDOS and the average signal magnitude is deduced.
The individual normalized Cy3 signals were averaged between the three replicates and the average signal was compared to the averaged reference Chinese Spring Cy5 signals.
The difference in the average signal between the normal and tumor regions for the fresh brain tissues was four times larger than those for the paraffin-embedded brain tissues.
For gene displaying an even number of exons the middle exonic RPKM was computed as the average signal between the two central exons whereas for genes displaying an odd number of exons the signal corresponding to the central exon was used.
It means that the average signal
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