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These scores were then tested for association with skin lesion status using mixed linear regression models adjusting for sex, age, and genotyping batch implemented in genome-wide efficient mixed model association (GEMMA) (Zhou and Stephens 2012).
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Pairwise linkage disequilibrium between each pair of loci (36 pairwise comparisons) within each population was tested using a Markov chain method (100,000 burn-in steps and 1,000 batches at 10,000 iterations per batch) as implemented in GENEPOP.
The value of 0 for the factor batch in Figure S1b indicates that the data has been adjusted for batch effects (implemented in Partek Genomics Suite 6.6; see methods).
Besides the duplication of the batch units implemented in previous works, the model considers the inclusion of intermediate storage tanks.
The studied learning rules for the models were the gradient descent adaptation (GD) and Levenberg-Marquardt batch optimization implemented as real-time retraining technique.
The case study considers the adaptive optimal design of 4 parallel fed-batch strategies implemented in 8 mini-bioreactors.
We suggest that accounting for known or unknown sources of variation, such as variable RNA integrity and batch, by implementing ComBat or Surrogate Variable Analysis for analysis of differential gene expression enables robust analysis of microarray datasets derived from variable and low quality RNA, thereby extending the range of clinical samples that are suitable for microarray analysis.
Furthermore, the batch effect correction implemented leads to a substantial increase in the sensitivity of statistical tests.
These potential benefits show significant advantages over the currently implemented batch methods which suffer from significant intermediate storage, high quantities of waste and intensive labour requirements.
A batch study was implemented to compare and optimize the biosorption process using n-Fe3O4-Phth S. aureus versus dried S. aureus for removal of Pb II), Ni II) and Cu II).
Batch processing is implemented in both R [ 26] and S-Plus scripts [ 27].
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