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Over the years the technology has undergone a significant evolution, allowing a reliable identification of functional relation of co-expressed genes and a good estimation of expression level for particular genes [1], [2].
The "model-based approach for estimation of expression variation" [ 27], supported by the NormFinder software, estimates intra- and intergroup variation, and thus subdivision of the sample set in at least two coherent groups is required for the correct application of this approach.
Figure 2 summarizes the expression selectivity of the 16,359 transcripts that have sequencing depth for confident estimation of expression selectivity, and Table 3 contains the ten most abundant transcripts selectively expressed in different stages (The list of the top 20 most abundant transcripts is available as additional file 2).
Microarrays are widely used for estimation of expression of thousands of genes in a biological sample.
Because the standard deviation of negative control probes is approximately 200 on all chips, genes with expression levels <200 are considered in the same levels as background noise and are excluded from estimation of expression level changes.
For this reason, sequences were aligned both to a reference transcript database (for estimation of expression of well-annotated transcripts) and to the human genome (for estimation of total expression of all exons, whether annotated or not).
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If product unobservables are really an issue then the estimation of expressions 1 3 should yield biased estimates of (beta ).
Upon estimations of expression manifested by estrogen receptor β in reproductive and perimenopausal women, no significant differences were detected between the two groups of patients.
To have a better fit in the model for more precise estimations of expression values, we included 10 additional microarrays in data normalization and extraction.
One advantage of digital sequencing for the estimation of gene expression over differential gene expression estimation by microarray is that it provides a more precise quantitative estimation of relative mRNA levels for the most highly expressed genes.
A limitation of the approach used in our study is that microarray-based assessment of gene expression does not allow estimation of the expression of splice isoforms.
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