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Second, the annealing temperature of the linear amplification was set at a higher temperature of 62 °C to reduce the possibility of non-specific amplification.
Threshold for amplification was set to segmented log2ratio ≥0.5, and for high-level amplification to segmented log2ratio ≥1 for HER2+ tumors.
Amplification was set at 50 μV/div, and the high and low-pass filters at 10 kHz and 20 Hz, respectively.
Threshold for amplification was set to segmented log2ratio ≥0.5, and for high-level amplification to segmented log2ratio >0.8 for HER2- tumors in the reference data set.
The cut-off for amplification was set at six gene copies per cell or the presence of a typical gene copy cluster [ 13].
The threshold for loss was set to segmented log2 ratio less than −0.32, gain was set to segmented log2 ratio ≥0.5, and amplification was set to segmented log2 ratio ≥0.85.
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The sampling frequency was set to 125 sps, the pre-amplification gain was set to 1 and the duration of each record was 20 25 min long.
The singers are miked and the amplification is set quite high.
The time sampling and amplification were set to 200 Hz and 500 times, respectively.
Thresholds for amplification and high-level amplification were set similarly as for BAC aCGH data.
Reactions with no amplification were set to an arbitrary CT of 45, and relative expression levels were calculated by the ΔΔCt method.
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