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While a few ad-hoc procedures have been suggested in the literature [ 41, 42], neither of them addresses how to control the false discovery rate, that is the amount of calls that are merged mistakenly because of random effects.
Successful protein identification may not have occurred because the detection of lower abundance peptide ions may have been masked by the presence of higher abundance ones, or because of random effects during the mass spectral analysis.
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This presents a challenge for the KWS- data set because the vector of random effects of all the genotypes (g) contains both the vector of effects of the n1 genotyped lines (g1) plus the vector of the effects of the n2 non-genotyped lines (g2) and so has a larger dimension (n1+ n2) than n1.
The calculation of a coefficient of determination R2 for GLMM is not obvious because of the presence of random effects.
We did not evaluate the significance of random effects because they were a required part of our experimental design.
Because of the large number of random effects, which equals the number of SNPs in this study, a faster algorithm is employed in our approach based on (1) and (2).
The illustration of predicting 6-month mortality after TBI prompted the use of random effects meta-analysis because of the strong difference – beyond chance – in concordance probability among centers.
We chose this model because there were random effects on tapping tasks based on the implementation of random effects on tapping tasks analyzed in the context of statistical parametric mapping in normality.
Inappropriate model specification of random effects can compromise inference.
Correcting this led to a significant effect of incomplete blocks in 07NC, which was therefore included in the updated model (BLUPs from the previous analysis are expected to be less precise, because the random effects of incomplete blocks were confounded with the random effect of RILs).
The magnitude of this tree-to-tree variation is apparent in this study because when the random effects of site and tree were considered, the total amount of variation in SGA explained by the models almost doubled.
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