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In order to adjust for false discovery rate caused by repeated Mann-Whitney U testing, we used a type I error bootstrap correction with 1000 iterations per generation following an established procedure for large scale datasets coded by Matlab R2007b [36], [52], [54], [55].
Interaction effects in the additive and multiplicative methods were tested using logistic regression implemented in a JAVA coded software designed to handle large datasets (coded in our own lab and available upon request) which is a modified version of the GEIRA software [ 42].
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To understand what presidents and secretaries are up to when they travel, we used a dataset coded from information compiled by the State Department that covers all trips by the president since the early 20th century and by the secretary of state since the civil war.
In addition, a measure of socioeconomic status based on the postal code of the patient's residential area was included in the dataset, coded as quintiles of deprivations for each patient [ 20, 22, 23 ].
Completeness was checked by comparison with the compulsory ICD-10 encoding of the clinical diagnoses in the hospital discharge dataset (code I21.X with exclusion of non ST-elevation myocardial infarctions).
An example dataset (code named Barb) for PTM is displayed in Figure 1b, which was captured with a 50-light dome (i.e. n=50) similar to the one shown in Figure 1a.
In our original dataset code 8312 comprised 31,331 (37%) of RCC patients.
Analysis of individual genes of the PPRV coding region dataset, coding and noncoding region datasets, and partial N gene dataset are shown in Table 4.
In addition, the MK test [ 106] was applied to evaluate a possible correlation between polymorphism and divergence for the synonymous to non-synonymous variation ratio predicted by the Neutral Theory [ 105] only for the mtDNA dataset (coding sequences).
The integrated dataset, code and database schema are available on request from L.H. Affymetrix U95A oligonucleotide microarray [ 15] data for 12,587 consensus probes in 101 human tissue samples were downloaded from the Gene Expression Atlas website.
Compared with non-gap-coded datasets, gap-coded datasets only slightly altered the support values (either increased or decreased) and topologies, regardless of weakly supported or collapsed nodes (results not shown).
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