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By relaxing the p-value to a relatively more permissive threshold of 0.05 to detect even slight changes in expression among treatments, we identified ca. 11,000 differentially expressed signatures, indicating that about 29,000 signatures are consistently expressed with non-significant differences under the culture conditions used here.
An additional 349 SNPs were significant with the more permissive threshold of FDR < 0.1.
A q-value of 0.10 was used as a significant association threshold in addition to a more permissive threshold of 0.2.
Anyway, a more permissive threshold could be more adequate to this explorative study, in order to avoid the β (or type II) statistic error, with the risk to neglect interesting results.
The final analysis is performed at a more permissive threshold setting in dictionary formation to allow discovery of rare variants, capitalizing on the enhanced mapping sensitivity provided by the enriched reference sequence collection.
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In addition, most loci identified using more permissive thresholds showed significant associations with more than one phenotype.
But the average frequency threshold must be chosen carefully: more permissive thresholds will lead to finishing TE-like elements, and more strict thresholds may mask high-copy gene families.
When using more permissive thresholds for filtering the distribution of unannotated transcripts appears similar to the whole data (results not shown) illustrating that these putative lichen-specific transcripts really are key players in the molecular mechanisms underpinning anhydrobiosis.
If d is no more than 50 base pairs away from overlapping a coding region of d' that encodes for protein p, then we say that d is linked to p (the strict threshold of 50 base pairs was chosen to ensure high quality, however, as Figure 3 shows, more permissive thresholds can be used to extend the set of links formed between DNA and protein sequences).
An additional 51 SNPs were significant using a more permissive significance threshold (false discovery rate (FDR) < 0.1).
Next, we identified regions using a more permissive significance threshold based on the 10% false discovery rate (Benjamini and Hochberg, 1995), equivalent to p = 3.49 × 10−5 for RTW and p = 2.86 × 10−4 for expression PC1.
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