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Of a total of 15,036 SNPs genotyped in this study, 9,195 survived filtering on MAF (> = 0.05) and HWE (P > 0.0001).
With extremely stringent conditions (FDR < 0.3% and fold change > 3-fold), 436 genes survived filtering and were identified as significantly dysregulated by PM exposure (375 genes up-regulated and 61 genes down-regulated).
A total of 1563 SNPs survived filtering at MAF ≥0.05, with deviation from Hardy Weinberg equilibrium (at P > 0.01) and LD pruning (at 0.05) to remove identical SNPs, for a final 190, 172, 107, 81, 162, 160, 146, 118, 152, 139, and 137 SNPs on chromosomes 1 to 11, respectively.
To determine the sites used for amplification by PCR, the 442 ORFs that survived filtering in this fashion were then scanned using a local copy of Primer3 (Rozen and Skaletsky, 2000) for pairs of oligonucleotides 18 25 bases in length that were located downstream of the stop codon and approximately 600 base pairs upstream from the stop codon that had similar base compositions.
Similar(8)
The clinking, clanging metal horses won't fool anybody for long, but more than in previous BioShock games, they suggest an element of wildness can survive filtering through such a tame form.
It would be good to present, for example, the number of genes surviving filtering as a function of these tuning parameters and other sensitivity curves.
Authors' response: we have made figures showing how the number of genes surviving filtering and performance statistics changed as a function of tuning parameters, which was presented in Figure 4. 11.
Increased confidence in the average of two technical replicates was obtained by restricting proteins considered significantly changed to those with a coefficient of variation (standard deviation as a percentage of the mean) of less than 100%, where this filtering criterion alone reduced false positives surviving filtering in the null experiment from 74 to 24.
Over 90% of the raw reads survived quality filtering and trimming, resulting in 21.4 ± 2.8 million (mean ± S.D).
We obtained approximately 2.33 million raw paired-end reads of which 2.29 million reads survived quality filtering and trimming as described above.
This in itself is bad news for Blumenthal and the Fat Duck, though it's worth bearing in mind that shellfish, which mostly survive by filtering microscopic algae and plankton from seawater, are notorious for storing up a variety of evils in their tissues and organs.
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