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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.
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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].
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].
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].
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.
As a first test of the probe-set method, we focused on enzymes with well-defined functions.
On the one hand, the τD measurements on entire genomic DNA represent a very strong test of the probe selectivity.
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.
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