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While some sources of variation have measurable influence on individual microarray signals, they showed very low influence on sample-to-reference ratios based on averaged triplicate measurements in the two-color experiments.
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FPKM was first proposed by Mortazavi et al. [ 34] and has been widely used as the gene expression levels by many studies [ 25, 27], as they have higher sensitivity and accuracy than microarray signals.
The microarray signals were analyzed using the Affymetrix RMA algorithm.
Microarray signals were analysed using a rank based statistic, Rank products (RP) [11].
As expected, microarray signals from liver samples were generally weaker than those of prostate samples (Figure 1).
Microarray signals flagged as "not positive and significant" or as "not above significant" were defined as "absent".
The Ct values correlate with expression levels derived from mRNA microarray signals reported in FlyAtlas (Fig. 1B).
We have applied the principles of stochastic resonance to detect expression of genes from microarray signals below the background noise level.
After 1 h incubation, unincorporated dye was removed using CentriSep spin columns (Princeton Separations, Inc .. Hybridization and detection of microarray signals was performed as described [19].
Finally, probes that produced significantly high microarray signals – exceeding the background value at least 3-fold in one or more of the pooled target samples – were selected.
Thus, 99.8% of unrelated probes had signal values that did not exceed 3X background (calculated as the lowest 5% of all signals), which was our cutoff for positive microarray signals.
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