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Using a stringent threshold of r2 = 1.0 (that is complete LD), the average number of proxies per SNP is 2.5, and one in two SNPs have five or more proxies.
We identified a group of 1,282 probe sets showing statistically significant differences in levels of expression between the five times with the Significance Analysis of Microarrays (SAM) method [2], using a stringent threshold false discovery rate (FDR) <0.01%.
In total, 2,530 up-regulated and 2,488 down-regulated genes were identified (Figure 2B) using a stringent threshold value to minimize the number of false positives (FDR below 0.25%).
Few data points deviated from expectation when using a stringent threshold value of 0.001 (Fig. 5 and Table V).
Using a stringent threshold (false discovery rate (FDR) = 0.05; see Methods) we found 302 Ndtargetrgenesenes (Additional file 1).
Using a stringent threshold of 1e-5, 80% identity and 80% coverage resulted in 2.6% BES matches to chloroplast/mitochondria (Table 2).
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We use a stringent threshold (score > 0.9999) to assign a sample as a VINO.
We used the interquartile range as a robust estimate of gene variation and used a stringent threshold at interquartile range = 0.75 (2,418 genes remaining).
We therefore used a stringent threshold and excluded cases where Vn_Simi and Vn_Syni were separated on the genomes by less than 10 genes.
[Here we used a stringent threshold, 20, which can achieve TP = 52.3%; FP = 26.7% for negative sample of protein coding DNA sequence, 5.21% for permuted sequences, and 12% for randomly generated intergenic sequences].
Moreover, even though we also use a stringent threshold in the overlapping filter (only e-CCC-Biclusters overlapping less than 25% are further analyzed), other overlapping thresholds can be used, thus allowing the analysis of a larger number of e-CCC-Biclusters, although potentially increasing the number of redundant biclusters.
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Justyna Jupowicz-Kozak
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