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Compared to the minor allele frequency (MAF) distribution of the complete set of variants of the 600 k array where only 3.8% of the variants detect rare alleles with a MAF < 0.05, OTVs showed with 40.8% rare alleles (MAF < 0.05) a reduced bias towards intermediate allele frequencies.
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These were analyzed using 3 K BAC and PAC arrays where only spots with signal intensities of at least two times the background intensities were included ([ 17], GSE5336, see Additional file 2).
Irizarry et al. compared different dilutions of 3 cell lines analyzed at 10 different laboratories and 3 different platforms (Affymetrix oligo arrays, 2-color oligo arrays and 2-color cDNA arrays where only one platform was employed by a given lab) and found that overall level of accuracy and precision of a given technological platform are greatly affected by the differences in lab performance.
Since obtaining whole genome sequences until recently was very costly, genomic studies have mostly relied on single nucleotide polymorphism (SNP) marker arrays, where only a small fraction of polymorphisms are preselected to be highly polymorphic and to cover the whole genome [ 2].
These simulations showed 4-fold enhanced retention of analytes (on entire available binding area) and 2-fold for high affinity ligand, compared to arrays where only the top planar surfaces support moderate affinity ligands (see Figure S1 in the Supporting Information).
Usually, the templates consist of a 2D array of pits where only a single island develops at the pit bottom [8].
To reduce this 'signal-to-noise' problem, we developed the Whole Genome Focused Array SNP Typing (WG-FAST) method, where only known SNPs with defined allele states are scored.
This is illustrated by canine chondrodysplasia and hyperuricosuria where only single SNPs on this array had significant association with the phenotype.
The 51 DAB sample is the only sample used on the peach array where lignification was readily detected.
Only ORFs that display at least a two-fold change, by either qRT-PCR or array, are included; except the 4 hour DTT treatment, where only the top ten hits are shown.
The array takes on more characteristics of a far-field array where the vertical direction MLW is so large that one only considers the angle or look direction instead of a focal point.
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