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Related Concept Videos

DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
Controls in Experiments01:13

Controls in Experiments

When conducting an experiment, it is crucial to have control to reduce bias and accurately measure the dependent variables. It also marks the results more reliable. Controls are elements in an experiment that have the same characteristics as the treatment groups but are not affected by the independent variable. By sorting these data into control and experimental conditions, the relationship between the dependent and independent variables can be drawn. A randomized experiment always includes a...
Quality Assurance01:19

Quality Assurance

Quality assurance is the overarching term used to describe the activities employed to ensure the proper performance of a system. These activities can be classified into three categories: quality control, quality assessment, and internal corrective measures. Typically, these activities work cyclically: quality control is performed before and during the analysis, while quality assessment occurs during and after the investigation. Internal corrective measures are implemented based on the findings...
Types of Biopharmaceutical Studies: Controlled and Non-Controlled Approaches01:23

Types of Biopharmaceutical Studies: Controlled and Non-Controlled Approaches

Biopharmaceutical studies constitute a vital field aiming to enhance drug delivery methods and refine therapeutic approaches, drawing upon diverse interdisciplinary knowledge. In research methodologies, the choice between controlled and non-controlled studies significantly influences the study's reliability and accuracy.
Non-controlled studies, commonly employed for initial exploration, lack a control group, rendering them susceptible to biases and external influences. In contrast, controlled...

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DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning
09:27

DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning

Published on: March 15, 2011

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

Katrice A Lippa1, David L Duewer, Marc L Salit

  • 1Chemical Science and Technology Laboratory,National Institute of Standards and Technology (NIST) Gaithersburg, Maryland 20899 USA. katrice.lippa@nist.gov.

BMC Research Notes
|December 30, 2010
PubMed
Summary
This summary is machine-generated.

External and internal RNA controls effectively assess microarray data quality, mirroring whole-array metrics. This supports their use for routine performance monitoring in gene expression studies.

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Gene expression microarray technology is advancing, necessitating robust quality assessment for clinical applications.
  • Current methods for assessing microarray data quality require quantitative measures for reliability.
  • Affymetrix GeneChip platform performance evaluation is crucial for diagnostic applications.

Purpose of the Study:

  • To characterize approaches for assessing the technical performance of microarray data.
  • To evaluate the utility of external spike-in and internal controls for quality assessment.
  • To compare the information content of various controls with whole-array metrics.

Main Methods:

  • Retrospective study analyzing Affymetrix GeneChip data.
  • Utilized a layered Principal Component Analysis (PCA) modeling methodology.
  • Incorporated data from spike-in hybridization, spike-in polyA+, internal RNA degradation, and endogenous housekeeping genes.

Main Results:

  • External spike-in controls provide information comparable to whole-array metrics and endogenous controls.
  • Controls offer insights into multiple experimental stages, including hybridization and RNA amplification.
  • Variance in control data is critical for technical performance assessment and aligns with QA/QC metrics.

Conclusions:

  • External and internal RNA controls are valuable for assessing microarray experiment technical quality.
  • Consistency between control data and whole-array measures enables reliable performance monitoring.
  • Development of rationally-designed control standards for multiplexed measurement platforms is promising.