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Since the IA evolves slowly, its mean or minimum amount during the segment can be utilized for normalization.
Although the mass of input RNA should not be utilized for normalization purposes, the amounts of input RNA to be assayed were equivalent.
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Signals obtained from U6 were utilized for normalization, and relative gene expression were analyzed by using the 2-ΔΔCT method [ 27].
Bioconductor DESeq package version 1.10.1 [ 38] was utilized for normalization, using the median log deviation, and for the differential expression analysis, applying a two-fold change cut-off, i.e. log2-fold change ≥ 1 or ≤ −1 and an adjusted p-value ≤ 0.05 were used as thresholds.
This mask retained the structural information of the T1-weighted image and could be utilized for defining normalization parameters.
Two color PCR reaction was utilized for the normalization of gene expression by the housekeeping gene TBP.
Chromosomes 7 and 8 did not show any interstitial aberrations or whole chromosome aberrations, so 4990 probes on these two chromosomes were utilized for the normalization.
Four internal controls were utilized for RT-qPCR result normalization: artificial miR-39 from C. elegans, U6 snRNA, miR-16 and snoRNA U91.
Four internal controls were utilized for qRT-PCR result normalization: an alien spike (artificial miR-39 from C. elegans) and three endogenous controls – U6 snRNA, miR-16 and snoRNA U91.
An arbitrary threshold was utilized for two reasons: first, to account for normalization errors, and second, to account for the fact that replicate data did not result from repeated hybridizations with the same RNAs but from repeated probe spotting.
Following the recommendations of [ 31], a normalization method based on robust local regression (lowess) was utilized for this purpose.
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