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Exact(4)
However, in our analysis we applied a more conservative minimum intensity threshold (i.e. log2 intensity ≥2) in order to reduce the potential for false positives and focus on miRNAs that could be said to be expressed with a high degree of confidence.
Only peaks above a minimum intensity threshold were selected based on a computationally estimated FDR of 0.1%.
Processing of the data from 108 spotted cDNA microarrays included background subtraction and log2-transformation of fluorescence intensities, and removal of flagged spots or spots that did not surpass a minimum intensity threshold of 200.
The minimum intensity threshold for MS/MS fragmentation in the Orbitrap analyzer was 5000 counts and the dynamic exclusion was set to 60 sec with repeat count as one.
Similar(56)
Using the matched L2-poly(A) samples, a pseudogene was called expressed if it passed a minimum array intensity threshold of 100 or minimum read count of 1.
Beta-values with detection P-value >0.01 are considered to fall below the minimum intensity and threshold and were consequently removed from further analysis.
This distribution offers the additional advantage that a minimum peak intensity threshold, which is naturally applied in peak picking, can be directly integrated into the model.
40P = 40% of maximum intensity threshold.
We used these parameters when the threshold minimum intensity was 0.5.
Images were ultimately generated by setting for each considered m/z value the minimum intensity at 5% and the full intensity threshold at 100%.
Peak lists were generated using Extract-msn program in Bioworks package v3.1 (Thermo Electron) with the following parameters: minimum ion count threshold, 15; minimum intensity, 100.
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