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Exploring the use of internal and externalcontrols for assessing microarray technical performance.

ABSTRACT: BACKGROUND:The maturing of gene expression microarray technology and interest in the use of microarray-based applications for clinical and diagnostic applications calls for quantitative measures of quality. This manuscript presents a retrospective study characterizing several approaches to assess technical performance of microarray data measured on the Affymetrix GeneChip platform, including whole-array metrics and information from a standard mixture of external spike-in and endogenous internal controls. Spike-in controls were found to carry the same information about technical performance as whole-array metrics and endogenous "housekeeping" genes. These results support the use of spike-in controls as general tools for performance assessment across time, experimenters and array batches, suggesting that they have potential for comparison of microarray data generated across species using different technologies. RESULTS:A layered PCA modeling methodology that uses data from a number of classes of controls (spike-in hybridization, spike-in polyA+, internal RNA degradation, endogenous or "housekeeping genes") was used for the assessment of microarray data quality. The controls provide information on multiple stages of the experimental protocol (e.g., hybridization, RNA amplification). External spike-in, hybridization and RNA labeling controls provide information related to both assay and hybridization performance whereas internal endogenous controls provide quality information on the biological sample. We find that the variance of the data generated from the external and internal controls carries critical information about technical performance; the PCA dissection of this variance is consistent with whole-array quality assessment based on a number of quality assurance/quality control (QA/QC) metrics. CONCLUSIONS:These results provide support for the use of both external and internal RNA control data to assess the technical quality of microarray experiments. The observed consistency amongst the information carried by internal and external controls and whole-array quality measures offers promise for rationally-designed control standards for routine performance monitoring of multiplexed measurement platforms.

SUBMITTER: Lippa KA

PROVIDER: S-EPMC3020182 | biostudies-literature | 2010 Dec

REPOSITORIES: biostudies-literature

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Exploring the use of internal and externalcontrols for assessing microarray technical performance.

Lippa Katrice A KA Duewer David L DL Salit Marc L ML Game Laurence L Causton Helen C HC

BMC research notes 20101228

<h4>Background</h4>The maturing of gene expression microarray technology and interest in the use of microarray-based applications for clinical and diagnostic applications calls for quantitative measures of quality. This manuscript presents a retrospective study characterizing several approaches to assess technical performance of microarray data measured on the Affymetrix GeneChip platform, including whole-array metrics and information from a standard mixture of external spike-in and endogenous i ...[more]

PMID: 21189145

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Project description:Purpose: Research establishing relationships between measures of rowing technique and velocity is limited. In this study, measures of technique and their effect on rowing velocity were investigated. Methods: Ten male singles, eight female singles, three male pairs, and six female pairs participated. Data from each stroke for forty-seven 2,000 m races were collected using Peach PowerLine and OptimEye S5 GPS units. General linear mixed modeling established modifying effects on velocity of two within-crew SD of predictor variables for each boat class, with subsequent adjustment for power, and for power and stroke rate in separate analyses. Twenty-two predictor variables were analyzed, including measures of boat velocity, gate force, and gate angle. Results were interpreted using superiority and inferiority testing with a smallest important change in velocity of 0.3%. Results: Substantial relationships with velocity were found between most variables assessed before adjustment for power, and for power and stroke rate. Effect magnitudes were reduced for most variables after adjustment for power and further reduced after adjustment for stroke rate and power, with precision becoming inadequate in many effects. The greatest modifying effects were found for stroke rate, mean and peak force, and power output before adjustment, and for catch angle after adjustment for stroke rate and power. Substantial between-crew differences in effects were evident for most predictors in some boat classes before adjustment and in some predictors and some boat classes after adjustment for stroke rate and power. Conclusion: The results presented reveal variables associated with improvements in rowing performance and can be used to guide technical analysis and feedback by practitioners. Higher stroke rates and greater catch angles should be targeted to improve rowing performance, and rower force development for the improvement of power output. Relationships between rowing technique and velocity can be crew-dependent and are best assessed on an individual basis for some variables.

Dataset Information

Exploring the use of internal and externalcontrols for assessing microarray technical performance.

Publications

Exploring the use of internal and externalcontrols for assessing microarray technical performance.

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