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As mentioned above, this can be accomplished by increasing the stringency settings of the calling algorithm [18].
As shown in Figure 2, the minimum accuracy of SIPHT predictions can be improved by increasing the stringency of the search parameters; however, as discussed above, this increased accuracy will often result in reduced sensitivity.
The observed distribution of the SNPs identified along the GA reads (Figures 1, 2) decreases towards the end of the reads indicating that we effectively filtered against false positives by increasing the stringency of removing low quality bases towards the end of the sequences.
In addition, by increasing the stringency of the false discovery rate (FDR) cutoff we further increased the percentage overlap.
In classical hybridization experiments, cross-hybridizing sequences can be distinguished from identical sequences by increasing the stringency of hybridization conditions.
We can even more closely approximate the number of high-confidence-only synapses by increasing the stringency of the classifier (a difference of <1%).
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We attempted to control for this possibility in three ways: i-by progressively increasing the stringency of the Pearson correlation coefficient threshold used to consider pairs of genes as coexpressed, ii-by using an independent metric for comparing gene expression vectors and iii-by building random coexpression networks using permuted gene expression datasets.
For example, when P = 0.05 were adopted in SF analysis at the greatest map density, average prediction ability was 0.21, and this improved to 0.31 by increasing the selection stringency to P = 0.01 (the first column of Figure 2).
By increasing the classification stringency, the GO terms were classified into 31 clusters, among which only two yielded significant Bonferroni corrected p-values including Embryoinic and skeletal system development and HOX genes (enrichment scores 6.48 and 5.52, respectively).
IPs were carried out, first with monoclonal anti-FLAG antibody followed by anti-PfSUMO sera, thus increasing the stringency of the purification.
We assessed the effect of increasing the stringency of vocabulary filtering by testing three thresholds of baseline cut-off ("c"), i.e.: 0.25, 0.05, and 0.01.
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