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As shown in Figure S3, a batch of samples processed together could have different RUD values than another batch which was not consistent with biological grouping.
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Each batch of the samples processed contained controls and cases in an approximate 12/7 ratio as previously described.
In this data there are two experiments, one that includes microarray data for four batches of control samples processed at the University of Cincinnati and a second that includes microarray data for patients with muscular dystrophy processed in five batches at UC Davis.
Ideally, CNV analysis of normal tissue samples processed simultaneously with the tumour specimens would eliminate technical noise variability and batch effects [ 29].
To ascertain whether the presence of lipids in solution could result in the retention of solvent, a separate batch of samples and blanks was processed with C-enriched methanol.
Automated analysis with a fluorescent threshold value set to 40 units yielded 2694 fragments, but the results were compromised by the fact that the restriction and ligation reactions had been carried out in two batches, as ten DNA samples became available only when the first batch of samples had already been processed.
An experiment often has many samples processed in multiple batches.
Each batch of samples was kept at room temperature, and processed the day immediately following blood collection, such that no samples were frozen or stored for longer than 24 h at room temperature.
Blanks were processed with each batch of samples.
A 3% HNO3 blank was processed in each batch of samples to control for possible contamination.
Positive and negative controls from the workflow control kit were processed with each batch of samples.
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