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Background median intensities were similar for all arrays except for the duck arrays, where the values were higher.
The thresholds for genome-wide significant association for all genotyping arrays (except for the Illumina HumanOmni2.5) range from 8.21 × 10−8 to 1.11 × 10−6, which are all slightly less stringent than the widely-adopted one, 5.0 × 10−8.
Expression differences were taken as the log2 of the red/green signal from the arrays, except for the comparison of unstressed cells, for which the array signal corresponding to unstressed wild-type or mig3 Δ cells was extracted from the ethanol arrays and normalized as described above.
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The confirmation rate was very low for most arrays except CytoSNP, for which 96.0% of the CNV calls were also seen on at least another array (Table 3).
Colour-magnitude and spectrum-magnitude diagrams can thus be plotted for the stars of a cluster, and the position of the stars in the array, except for a factor that is the same for all stars, will be independent of distance.
Spot signal intensity was determined after local background subtraction and normalised based on total signal intensity of all genes on the array except for genes encoding rRNAs.
The Barcoder array was designed to pair perfectly with the FLEX array except for a small number of negative controls that were eliminated through SGA.
For large genes, we chose to cover introns with a lower probe density (one probe each 300 bp) than exons (one probe each 40 bp) to save space on the array, except for the CFTR and DMD genes.
The coding sequences of these arrays were identical, except for very occasional silent changes.
Power is generally low for the range of parameters considered here (even for "1000 Genomes" array), except at the upper end of genetic effect and sample sizes.
As a control, all of the Affymetrix anatomical meta-expression profiles in the Rice Oligonucleotide Array Database (ROAD;), except for two anther samples, were used to check expression patterns in other tissues/organs (Cao et al. 2012).
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