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For each of the eight stringency zones, a normalized ratio for each probe pair was calculated as the signal from the wild-type probe divided by the sum of the signals from the wild-type and mutant probes (SWT/(SWT+SMT)).
The ratio was calculated as the number of signals for the gene probe divided by the number of signals for the centromere reference probe.
To estimate the CNR for a given sample at a given SNP probe, we computed the log2 ratio of the normalized intensity of this probe divided by the median across all the samples from the same batch.
Normalized index values were generated by dividing the average number of sequence reads in an 11 bp window around a particular base pair by the average coverage for the probe (the total sequence reads for a particular probe divided by the length of the probe).
Normalized nucleosome coverage index values were generated by dividing the number of sequence reads at a particular base pair by the average coverage for the probe (the total sequence reads for a particular probe divided by the length of the probe).
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The remaining significantly expressed probes, divided into up- and down-regulated subgroups, were uploaded onto the DAVID portal (http://david.abcc.ncifcrf.gov/home.jsp) for singular enrichment analysis in comparison with the list of protein sequences in the All-Pinus database.
The Nimblegen© array comprised of 387,835 50-75mer Probes divided into 122 regions covering 37,037,978 bases of the genome.
The z-score was calculated by taking the average glog ratio of a region, trying region sizes from one to ten probes, divided by the expected standard deviation of an average coming from an N 0,s) distribution.
Universal microarrays with 861 probes divided into two microarray slides were used.
This statistic gives the observed minus expected number of non-unique probes divided by the SD of a hypergeometric distribution.
For both the gain and diploid popLowess populations the total number of called probes divided by expected total number of probes from karyotyping data was calculated.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com