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Furthermore, we collapsed the matched clones representing the same gene by their mean expression value (Figure 1A).
Four pairs of technical replicate samples were summarized by their mean expression profiles.
Multiple probes assigned to the same RefSeq ID were summarized by their mean expression profile.
Four probes replicated within and between bead sets and three pairs of technical replicate samples were summarized by their mean expression profiles.
To better measure the impact of large-scale genomic alterations on gene expression we divided the expression values for genes located within aneuploid regions by their mean expression in the tumors without the analyzed alteration.
Thus, the laboratory and industrial variants of these promoters differed by their mean expression in at least one background, but enhanced expression did not necessarily produce lower noise so that the genetic variations might generate a different level of noise at similar mean expression level.
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Probesets with the greatest variation across all tissues and whose expression in at least two samples differed by two standard deviations from their mean expression across the entire set of samples were selected.
For each condition, differentially expressed genes were sorted by their mean normalized expression ratio in ascending or descending order.
Data were normalized by dividing all replicates by their mean transcript expression level and multiplying by 1000, and then loaded in the R/MAANOVA package (http://research.jax.org/faculty/churchill/software/Rmaanova/index.html).html
Candidate reference miRNAs were identified by their correlation with global mean expression.
To identify the most differentially expressed genes, we sorted the "selective" gene sets by their fold change of mean expression and classified them in 14 functional categories.
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by their mean firing
by their reduced expression
by their tdRFP expression
by their mean function
by their mean coverage
by their distinctive expression
by their relative expression
by their mean probability
by their absolute expression
by their mean population
by their specific expression
by their mean S-score
by their mean area
by their differential expression
by their altered expression
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