Feb 11, 2015

Using Mixtures of Biological Samples as Process Controls for RNA-sequencing experiments

BioRxiv : the Preprint Server for Biology
Jerod ParsonsMarc Salit

Abstract

Genome-scale ?-omics? measurements are challenging to benchmark due to the enormous variety of unique biological molecules involved. Mixtures of previously-characterized samples can be used to benchmark repeatability and reproducibility using component proportions as truth for the measurement. We describe and evaluate experiments characterizing the performance of RNA-sequencing (RNA-Seq) measurements, and discuss cases where mixtures can serve as effective process controls. We apply a linear model to total RNA mixture samples in RNA-seq experiments. This model provides a context for performance benchmarking. The parameters of the model fit to experimental results can be evaluated to assess bias and variability of the measurement of a mixture. A linear model describes the behavior of mixture expression measures and provides a context for performance benchmarking. Residuals from fitting the model to experimental data can be used as a metric for evaluating the effect that an individual step in an experimental process has on the linear response function and precision of the underlying measurement while identifying signals affected by interference from other sources. Effective benchmarking requires well-defined mixtures, which for R...Continue Reading

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Mentioned in this Paper

Genome
Sequence Determinations, RNA
Evaluation
Sequencing
RNA, Messenger
Genome Sequencing
RNA
Research Study
Protein Expression

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