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By application of a stringent signal to noise test (as detailed below), the overwhelming majority of spurious data is removed since they commonly display features of poor signal intensity.
This step included the adaptor removal as well as the application of a stringent filtering criterion to remove reads with >10% unknown bases and remove low quality reads, i.e. reads that comprise at least 50% low-quality bases.
Application of a stringent set of SNP filtering criteria to remove the bias and restriction of the association analysis to the 48,035 SNPs that fulfilled all filtering criteria resulted in a low inflation rate (λGC 1.05) (ESM Fig. 9).
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For identifying unexpected species, the application of a less stringent metagenomic search tool, based on a BLAST database search followed by visualization via MEGAN, also proved successful.
The amount of FPs associated to an arbitrary p-value threshold of 0.05 is in both cases very high (Table 2) and the application of a more stringent p-value threshold reduces the number of FPs but also impacts negatively on TP rate (data not shown).
Finally, an obvious application and a stringent test of PS sequencing is whole-genome de novo assembly, which will be reported below.
Application of these stringent criteria resulted in a total population of 1937 women.
Application of more stringent cut-off levels revealed an average consistency of 368 (75%) and 153 (72%) differentially expressed genes between one and two rounds of amplification at a cut-off level of 3×SD (p < 0.003) and 4×SD (p < 0.0001) respectively.
In the light of these findings, we aimed to evaluate the clinical significance of ERBB2 expression in a large group of advanced stage ovarian carcinomas, with the application of less stringent criteria of ERBB2 overexpression, and with respect to TP53 status.
The application of similarly stringent in silico quality filters to the initial SNP source also caused a 10-fold reduction in the available putative SNP when developing a 54,000 SNP array for bovine, but resulted in an increase from 50%to>85%5% in the conversion rate [ 50].
The significant number of potential lead sequences allowed for the application of more stringent lead criteria such as good solubility, high peptide sample purity and low background binding to the SPR chip surface.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com