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Reproducibility and reliability assays of the gene expression-measurements.

ABSTRACT: BACKGROUND:Reliability and reproducibility are key metrics for gene expression assays. This report assesses the utility of the correlation coefficient in the analysis of reproducibility and reliability of gene expression data. RESULTS:The correlation coefficient alone is not sufficient to assess equality among sample replicates but when coupled with slope and scatter plots expression data equality can be better assessed. Narrow-intervals of scatter plots should be shown as a tool to inspect the actual level of noise within the data. Here we propose a method to examine expression data reproducibility, which is based on the ratios of both the means and the standard deviations for the inter-treatment expression ratios of genes. In addition, we introduce a fold-change threshold with an inter-replicate occurrence likelihood lower than 5% to perform analysis even when reproducibility is not acceptable. There is no possibility to find a perfect correlation between transcript and protein levels even when there is not any post-transcriptional regulatory mechanism. We therefore propose an adjustment for protein abundance with that of transcript abundance based on open reading frame length. CONCLUSIONS:Here, we introduce a very efficient reproducibility approach. Our method detects very small changes in large datasets which was not possible through regular correlation analysis. We also introduce a correction on protein quantities which allows us to examine the post-transcriptional regulatory effects with a higher accuracy.

SUBMITTER: Darbani B

PROVIDER: S-EPMC4376515 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature

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Reproducibility and reliability assays of the gene expression-measurements.

Darbani Behrooz B Stewart Charles Neal CN

Journal of biological research (Thessalonike, Greece) 20140513 1

<h4>Background</h4>Reliability and reproducibility are key metrics for gene expression assays. This report assesses the utility of the correlation coefficient in the analysis of reproducibility and reliability of gene expression data.<h4>Results</h4>The correlation coefficient alone is not sufficient to assess equality among sample replicates but when coupled with slope and scatter plots expression data equality can be better assessed. Narrow-intervals of scatter plots should be shown as a tool ...[more]

PMID: 25984486

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Project description:The advantages of intraoral model scanning have yielded recent developments. However, few studies have explored the orthodontic clinical use of this technique particularly among young patients. This study aimed to evaluate the reliability, reproducibility and validity of the orthodontic measurements: tooth width, arch length and arch length discrepancy in each digital model obtained by model scanner and intraoral scanner, relative to a plaster model. Arch length measured using two methods: curved arch length (CAL) measured automatically by digital program and sum of sectional liner arch length (SLAL) measured sum of anterior and posterior liner arch lengths. Arch length discrepancy calculated each arch length measurement methods: curved arch length discrepancy (CALD) and sum of sectional liner arch length discrepancy (SLALD). Forty young patients were eligible for the study. A plaster model (P), model-scanned digital model (MSD) and intraoral scanned digital model (ISD) were acquired from each patient. The reliability of the measurements was evaluated using Pearson's correlation coefficient, while the reproducibility was evaluated using the intraclass correlation coefficient. The validity was assessed by a paired t-test. All measurements measured in P, MSD and ISD exhibited good reliability and reproducibility. Most orthodontic measurements despite of CAL in MSD exhibited high validity. Only the SLAL and SLALD in ISD group differed significantly, despite the good validity of the tooth width, CAL and CALD. The measurements based on the digital program appeared high reliability, reproducibility and accurate than conventional measurement. However, SLAL and SLALD in ISD group appeared shorter because of distortion during intraoral scanning. However, this could be compensated by using digital programed curved arch. Although the validity of SLAL and SLALD in the ISD group differed statistically, the difference is not considered clinically significant. Although MSD and ISD are acceptable for a clinical space analysis, clinicians should be aware of digital model-induced errors.

Project description:INTRODUCTION:Quantitative longitudinal magnetic resonance imaging and spectroscopy (MRI/S) is used to assess progress of brain disorders and treatment effects. Understanding the significance of MRI/S changes requires knowledge of the inherent technical and physiological consistency of these measurements. This longitudinal study examined the variance and reproducibility of commonly used quantitative MRI/S measurements in healthy subjects while controlling physiological and technical parameters. METHODS:Twenty-five subjects were imaged three times over 5 days on a Siemens 3T Verio scanner equipped with a 32-channel phase array coil. Structural (T1, T2-weighted, and diffusion-weighted imaging) and physiological (pseudocontinuous arterial spin labeling, proton magnetic resonance spectroscopy) data were collected. Consistency of repeated images was evaluated with mean relative difference, mean coefficient of variation, and intraclass correlation (ICC). Finally, a "reproducibility rating" was calculated based on the number of subjects needed for a 3% and 10% difference. RESULTS:Structural measurements generally demonstrated excellent reproducibility (ICCs 0.872-0.998) with a few exceptions. Moderate-to-low reproducibility was observed for fractional anisotropy measurements in fornix and corticospinal tracts, for cortical gray matter thickness in the entorhinal, insula, and medial orbitofrontal regions, and for the count of the periependymal hyperintensive white matter regions. The reproducibility of physiological measurements ranged from excellent for most of the magnetic resonance spectroscopy measurements to moderate for permeability-diffusivity coefficients in cingulate gray matter to low for regional blood flow in gray and white matter. DISCUSSION:This study demonstrates a high degree of longitudinal consistency across structural and physiological measurements in healthy subjects, defining the inherent variability in these commonly used sequences. Additionally, this study identifies those areas where caution should be exercised in interpretation. Understanding this variability can serve as the basis for interpretation of MRI/S data in the assessment of neurological disorders and treatment effects.

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Reproducibility and reliability assays of the gene expression-measurements.

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Reproducibility and reliability assays of the gene expression-measurements.

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