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For a multi-parametric test of probe choice strategies for genotyping with ASH-based assays, we combined custom made (Agilent) high-density microarrays with an in-house multi-stringency array washer which has been described in [13].
Consolidating sibling probe sets is determined automatically through statistical test of probe set by treatment interaction effect in the two-way ANOVA model.
The method described by Kirst et al. using a test of probe × variety interaction as an indication of the presence of a SFP was used to analyze the PM probe signal intensities [ 35].
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The Agilent 8x15K array format was chosen for the experiment because it allowed a multi-parametric test of probes for genotyping (about 15,000 probes/sub-array) in combination with multi-stringency washes of the eight identical sub-arrays, thereby maximizing the data output, and making the experiment practically and economically feasible.
For the MA described here, the empirical tests of probe specificity (Additional file 2: Figure S1) and the probe design parameters appeared sufficient to discriminate between paralogs that are known in the P. glauca catalogue of 27,720 genes [ 13].
Further, to promote the selective, economic and easy detection of hydrazine, the fluorescent test strips of probe 2 have been prepared which can detect hydrazine up to femtogram level.
More elaborated software tools include cross-homology testing of probes against a reference database by BLAST (Basic Local Alignment Search Tool) [ 9, 10] or prediction of secondary structures into the thermodynamically-based approach [ 11- 14].
Any probe set with a probability of less than 1e-10 for the F test of the probe × variety effect was selected as potentially polymorphic.
Our first test of this probe is to help find and excise sentinel lymph nodes.
On the one hand, the τD measurements on entire genomic DNA represent a very strong test of the probe selectivity.
By employing nano- and micro-scale tribological testing with probes of differing sharpness it is possible to change the sensitivity of the test to probe the response of the coating top layer or the entire multilayer coating substrate system.
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