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In order to assess statistically significant species concordance across different effects, a permutation study was carried out.
Large (classified as those >500 kb) and rare (<1% frequency) CNVs were used in this analysis because they are called with greater accuracy, have better concordance across different platforms, and show the most robust associations with neurodevelopmental disorders (5).
A series of studies have been reported on evaluating performance across various commercial and home-brewed microarray platforms, however, most of these studies focused on evaluating the level of concordance across different microarray platforms.
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Variant calls were analyzed with a specialized workflow that accounts for the inheritance structure and concordance across the different methods.
This approach afforded the most straightforward study of the concordance across the different platforms and did not favor platforms with high feature-to-target and/or target-to-transcript ratios.
52– 60 Despite their reported low level of concordance across the different datasets, Hecker et al 13 showed that by integrating multiple datasets, they could reconstruct a majority of the links between the seed network genes simply on the basis of observed correlations between genes in multiple (at least 2 out of 5) gene expression datasets (recreated using BioNetwork Bench, Table 1).
Of 13 studies, 8 produced results supporting the reproducibility and concordance of data across different microarray technologies.
This lack of concordance and consistency across different utility measures to assess overall health status has been frequently described in the literature.
For example, one study reported that RNA-seq data are highly consistent as long as the same laboratory protocols and versions of sample preparation and sequencing kits are used [ 4], and another study reported high intra-platform concordance when testing different protocols across different sequencing platforms for the same samples [ 5].
In addition to absolute DNA methylation levels, we also analyzed the difference in methylation levels across different individuals measured using the same technology, and compared the concordance of this difference across the two platforms.
Consistent with this, we found limited concordance in parity-related gene content results across different signatures.
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