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Fixing the topology to the tree obtained by MVS, which is very similar to trees obtained by previous authors using varied data sets [2] [5], branch lengths were reestimated using maximum likelihood (ML) in the program PAML [35].
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In the stratified analyses, heterogeneity between studies was reduced, suggesting that the varied data collection method, recruitment setting, sample size, study time and study locations may account for the inconsistency among studies.
Because the original limit of quantification (LOQ) varied between data sets, we had to recalculate uniform LOQs for the present study.
SAMOVA analyses of haplotypic data consistently separated LM from other localities regardless of the data set used, although the optimal number of groups was generally 3 and the third group varied between data sets (Additional file 1: Table S4).
The smallest number that will give acceptable performance will depend on the experimental noise of the data and may vary between data sets.
Note that m only varies between data sets and not during training or feature selection processes.
SEH (Appendix S2) values reveal the most distinct species, which vary between data sets as the plant composition changes.
In all cases the regression collective, given enough data, is Bayes optimal if any one machine is so, and where this unnamed optimal machine in the portfolio of the collective can vary over data sets.
all SAMs were calculated using covariates of the primary analysis; number of observations vary in data sets and between steps of the regression model: f.s.: primary analysis, SAM2, SAM3, SAM4 (N = 3356), SAM1 (N = 3355).
The Affymetrix compendium described above was curated and filtered for genes that were present in all data sets, as well as genes that vary in their expression across data sets.
The main disadvantage of the RIE method is its minimum and maximum value which are not intuitive and which vary from data set to data set.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com