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Our analysis method consisted of four steps: abundance quantization and filtering of probes; a feature selection algorithm to refine the probe selection; a Jensen-Shannon divergence computation; and finally, a correlation analysis.
Structuring elements are attributes that probes a features of interest.
Therefore each probe was attributed a feature number with corresponding numbers in the two annotations.
Chemical saturation, in which most or all of the oligos in a probe feature are bound by target DNAs, creates a nonlinear relationship between target concentration and probe intensity [ 29].
For convenience, a 25 bp probe will be referred to as a "feature" and a probe-set will be called "probe" in the rest of the paper.
Probes were mapped to a feature if there was any overlap between the probe and feature.
Therefore, we simply assigned the polymorphism to a feature (probe) and called it a single feature polymorphism (SFP) as described [ 28].
The probe features a 5′ and a 3′ propanyl abasic site and is designed as follows: 5′-thiol – poly(T6) – (N)11 – 5′ abasic site (5′-CXT) – (N 9 – 3′ abasic site (AXC-3′) – (N)7 – poly(T8 -3′.
Of these, 117 were represented by a probe set feature on the Affymetrix Human Genome U133 Plus 2.0 array and were thus considered in our analyses of psoriasis GWAS candidates.
Of these 395 genes, 357 were represented by a probe set feature included on the Affymetrix Human Genome U133 Plus 2.0 array and were thus included in our analyses (Additional files 13 and 14).
We write the probe image in terms of a feature vector.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com