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To verify our simulation result, we used SMRI data, in which nine factors are considered possible sources of variation and batch effects were divided into site and date effects separately.
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Batch effects were removed by aligning the within-batch medians for all measurements.
Batch effects were then adjusted by the COMBAT method [ 30].
Experimental batch effects were adjusted for by including experimental batch as a covariate in the statistical model [ 56].
(3) Can batch effects be controlled?
Batch effects are not the only source of unwanted variance.
They can also mistake population stratification of common CNVs for batch effects if true batch effects are minimal.
However for the design in Table 4, the batch effects are nested within sex and time effects and the result of disregarding batch effects can easily be evaluated.
Batches of embryos were divided to perform embryonic, larval and adult investigations.
The HTP experiments were divided into nine batches, in each batch, 15.0 g the extractive-free material was mixed with 150 mL deionized water.
For continuous ethylene monitoring, ethylene-treated fruit were divided into 6 batches of fruit per treatment (3 fruit per batch).
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